In [145]:
sc.pl.violin(adata, ['n_genes', 'n_counts', 'percent_mito'],jitter=0.4, multi_panel=True)
Goal: Compare clustering on PBMC data in order to regress bioinformatician bias
https://eleozzr.github.io/desc/tutorial.html DESC - The goal of this tool is to automatically identify the proper number of clusters within your single cell data according to the samples biological heterogeneity
Nevertheless, the main parameter that determines the number of clusters identified is the resolution of the clustering algorithm (typically louvain or leiden). A high resolution will identify a large number of clusters and a low resolution will identify a low number of clusters.
Consequently, we will incrementally iterate over the entire range of possible resolutions and compare the results because Control and scCLEAN.
import desc as desc
import numpy as np
import pandas as pd
import scanpy as sc
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
sc.set_figure_params(dpi=200, color_map = 'viridis_r')
sc.settings.verbosity = 3 # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.logging.print_versions()
WARNING: If you miss a compact list, please try `print_header`!
The `sinfo` package has changed name and is now called `session_info` to become more discoverable and self-explanatory. The `sinfo` PyPI package will be kept around to avoid breaking old installs and you can downgrade to 0.3.2 if you want to use it without seeing this message. For the latest features and bug fixes, please install `session_info` instead. The usage and defaults also changed slightly, so please review the latest README at https://gitlab.com/joelostblom/session_info. ----- anndata 0.7.8 scanpy 1.7.2 sinfo 0.3.4 ----- 2f7ece400a652629565c523b34ee61b04afa385c NA PIL 8.4.0 absl NA appnope 0.1.2 astunparse 1.6.3 backcall 0.2.0 cached_property 1.5.2 certifi 2020.06.20 cffi 1.15.0 charset_normalizer 2.0.9 cycler 0.10.0 cython_runtime NA dateutil 2.8.2 decorator 4.4.2 defusedxml 0.7.1 desc 2.1.1 dot_parser NA entrypoints 0.3 flatbuffers NA gast NA get_version 2.1 google NA h5py 3.1.0 idna 3.3 igraph 0.9.8 ipykernel 5.5.6 ipython_genutils 0.2.0 jedi 0.17.2 joblib 1.1.0 keras 2.6.0 keras_preprocessing 1.1.2 kiwisolver 1.3.1 legacy_api_wrap 1.2 llvmlite 0.36.0 louvain 0.7.0 matplotlib 3.3.4 mpl_toolkits NA natsort 8.0.1 numba 0.53.1 numexpr 2.8.1 numpy 1.19.5 opt_einsum v3.3.0 packaging 21.3 pandas 1.1.5 parso 0.7.1 pexpect 4.8.0 pickleshare 0.7.5 pkg_resources NA prompt_toolkit 3.0.24 ptyprocess 0.7.0 pydot 1.4.2 pygments 2.10.0 pyparsing 3.0.6 pytz 2021.3 requests 2.26.0 scipy 1.5.4 six 1.15.0 sklearn 0.24.2 storemagic NA tables 3.6.1 tensorboard 2.6.0 tensorflow 2.6.2 termcolor 1.1.0 texttable 1.6.4 threadpoolctl 3.0.0 tornado 6.1 traitlets 4.3.3 typing_extensions NA urllib3 1.26.7 wcwidth 0.2.5 wrapt 1.12.1 zipp NA zmq 22.3.0 ----- IPython 7.16.2 jupyter_client 7.1.0 jupyter_core 4.9.1 notebook 6.4.6 ----- Python 3.6.13 |Anaconda, Inc.| (default, Feb 23 2021, 12:58:59) [GCC Clang 10.0.0 ] Darwin-20.6.0-x86_64-i386-64bit 12 logical CPU cores, i386 ----- Session information updated at 2022-06-21 15:28
#input the cellranger output h5ad file from alignment to the full transcriptome
adata = desc.read_h5ad('raw_files/FUll_transcriptome/Control_not_masked_filtered_feature_bc_matrix.h5ad')
adata.var_names_make_unique()
adata
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
AnnData object with n_obs × n_vars = 11714 × 36601
var: 'gene_ids', 'feature_types', 'genome'
#perform simple, standard QC
sc.pp.filter_cells(adata, min_counts=500)
sc.pp.filter_cells(adata, min_genes=200)
sc.pp.filter_genes(adata, min_cells=3)
Variable names are not unique. To make them unique, call `.var_names_make_unique`. Variable names are not unique. To make them unique, call `.var_names_make_unique`. filtered out 230 cells that have less than 200 genes expressed Variable names are not unique. To make them unique, call `.var_names_make_unique`. Variable names are not unique. To make them unique, call `.var_names_make_unique`. filtered out 15194 genes that are detected in less than 3 cells Variable names are not unique. To make them unique, call `.var_names_make_unique`. Variable names are not unique. To make them unique, call `.var_names_make_unique`.
mito_genes = adata.var_names.str.startswith('MT-')
# for each cell compute fraction of counts in mito genes vs. all genes
# the `.A1` is only necessary as X is sparse (to transform to a dense array after summing)
adata.obs['percent_mito'] = np.sum(
adata[:, mito_genes].X, axis=1).A1 / np.sum(adata.X, axis=1).A1
# add the total counts per cell as observations-annotation to adata
adata.obs['n_counts'] = adata.X.sum(axis=1).A1
adata.obs
| n_counts | n_genes | percent_mito | |
|---|---|---|---|
| AAACCCAAGAACGTGC-1 | 4529.0 | 1306 | 0.036211 |
| AAACCCAAGACAGTCG-1 | 4158.0 | 1724 | 0.078163 |
| AAACCCAAGGACAACC-1 | 5419.0 | 1666 | 0.026020 |
| AAACCCAAGGTTTGAA-1 | 6235.0 | 1952 | 0.071532 |
| AAACCCAAGTTAACGA-1 | 3315.0 | 1527 | 0.085370 |
| ... | ... | ... | ... |
| TTTGTTGTCCACGGGT-1 | 10859.0 | 2888 | 0.067502 |
| TTTGTTGTCGAGGCAA-1 | 1654.0 | 830 | 0.220677 |
| TTTGTTGTCGAGTCCG-1 | 5177.0 | 1306 | 0.025304 |
| TTTGTTGTCGTTCAGA-1 | 3541.0 | 1450 | 0.097995 |
| TTTGTTGTCTTCGACC-1 | 5712.0 | 1604 | 0.034664 |
11484 rows × 3 columns
#determine the proper thresholds according to the 99% of the data
per_cell_metrics = adata.obs
quantile = pd.DataFrame()
quantile = per_cell_metrics.quantile(0.99, numeric_only=True)
quantile
n_counts 18648.920000 n_genes 4176.700000 percent_mito 0.122461 Name: 0.99, dtype: float64
sc.pl.violin(adata, ['n_genes', 'n_counts', 'percent_mito'],jitter=0.4, multi_panel=True)
#filter thresholds from 99%
adata = adata[adata.obs['n_counts'] < 18648.92, :]
adata
View of AnnData object with n_obs × n_vars = 11369 × 21407
obs: 'n_counts', 'n_genes', 'percent_mito'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells'
desc.normalize_per_cell(adata, counts_per_cell_after=1e4)
normalizing by total count per cell
Trying to set attribute `.obs` of view, copying.
finished (0:00:00): normalized adata.X and added 'n_counts', counts per cell before normalization (adata.obs)
desc.log1p(adata)
adata.raw=adata
sc.pp.highly_variable_genes(adata, min_mean=0.0125, max_mean=3, min_disp=0.5, subset=True)
extracting highly variable genes
finished (0:00:00)
--> added
'highly_variable', boolean vector (adata.var)
'means', float vector (adata.var)
'dispersions', float vector (adata.var)
'dispersions_norm', float vector (adata.var)
#According to DESC tutorial, recomends performing analysis on highly variable genes
adata = adata[:, adata.var['highly_variable']]
adata
View of AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
uns: 'log1p', 'hvg'
#the data has to be standardized prior to DESC
desc.scale(adata, zero_center=True, max_value=3)
/Users/jbezney/opt/anaconda3/envs/DESC/lib/python3.6/site-packages/scanpy/preprocessing/_simple.py:845: UserWarning: Revieved a view of an AnnData. Making a copy. view_to_actual(adata) ... as `zero_center=True`, sparse input is densified and may lead to large memory consumption
#loop through the deep learning model and append the total number of clusters identified
#check the total number of clusters according to the resolution with which it was identified
resolution_x = [0.1,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,1.8,2.0]
total_clusters = []
for value in resolution_x:
adata = desc.train(adata, dims=[adata.shape[1], 128, 32], tol=0.001, n_neighbors=10,
batch_size=256, louvain_resolution=[value], do_tsne=True, learning_rate=300,
do_umap=True, num_Cores_tsne=4)
df_cluster = pd.DataFrame(adata.obs['desc_'+str(value)])
df_cluster = len(df_cluster.iloc[:,0].unique())
total_clusters.append(df_cluster)
Start to process resolution= 0.1 The number of cpu in your computer is 12 WARNING:tensorflow:From /Users/jbezney/opt/anaconda3/envs/DESC/lib/python3.6/site-packages/desc/models/desc.py:123: The name tf.keras.backend.set_session is deprecated. Please use tf.compat.v1.keras.backend.set_session instead. Create the directory:result_tmp to save result Checking whether result_tmp/ae_weights.h5 exists in the directory The file ae_weights.h5 is not exits Pretraining the 1th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 1s 6ms/step - loss: 0.5051 Epoch 2/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4777 Epoch 3/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4559 Epoch 4/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4424 Epoch 5/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4326 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.4241 Epoch 7/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4169 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4113 Epoch 9/50 45/45 [==============================] - 0s 8ms/step - loss: 0.4064 Epoch 10/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4030 Epoch 11/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4000 Epoch 12/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3976 Epoch 13/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3955 Epoch 14/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3938 Epoch 15/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3924 Epoch 16/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3911 Epoch 17/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3900 Epoch 18/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3891 Epoch 19/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3882 Epoch 20/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3873 Epoch 21/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3866 Epoch 22/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3859 Epoch 23/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3852 Epoch 24/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3846 Epoch 25/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3842 Epoch 26/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3835 Epoch 27/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3830 Epoch 28/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3825 Epoch 29/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3819 Epoch 30/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3815 Epoch 31/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3810 Epoch 32/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3806 Epoch 33/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3800 Epoch 34/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3797 Epoch 35/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3792 Epoch 36/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3788 Epoch 37/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3784 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3782 Epoch 39/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3777 Epoch 40/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3773 Epoch 41/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3770 Epoch 42/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3767 Epoch 43/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3763 Epoch 44/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3761 Epoch 45/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3758 Epoch 46/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3754 Epoch 47/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3751 Epoch 48/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3749 Epoch 49/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3746 Epoch 50/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3744 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 1s 7ms/step - loss: 0.3741 Epoch 2/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3742 Epoch 3/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3741 Epoch 4/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3740 Epoch 5/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3740 Epoch 6/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3740 Epoch 7/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3739 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3741 Epoch 9/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3739 Epoch 11/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3739 Epoch 12/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 13/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3737 Epoch 14/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 15/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 16/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 17/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3737 Epoch 18/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3737 Epoch 19/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3736 Epoch 20/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 21/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3736 Epoch 22/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 23/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 24/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3735 Epoch 25/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3736 Epoch 26/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3735 Epoch 27/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3735 Epoch 28/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3735 Epoch 29/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3733 Epoch 30/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3734 Epoch 31/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3734 Epoch 32/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3734 Epoch 33/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3732 Epoch 34/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3733 Epoch 35/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3733 Epoch 36/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3733 Epoch 37/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3732 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3733 Epoch 39/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3732 Epoch 40/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 41/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 42/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 43/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3731 Epoch 44/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 45/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 46/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 47/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3730 Epoch 48/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 49/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3729 Epoch 50/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3730 learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 1s 7ms/step - loss: 0.3730 Epoch 2/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3731 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 4/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 5/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3730 Epoch 6/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3730 Epoch 7/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3729 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3731 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 11/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 12/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 13/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3728 Epoch 14/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3729 Epoch 15/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3729 Epoch 16/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3729 Epoch 17/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 00017: early stopping The 1th layer has been pretrained. Pretraining the 2th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 936us/step - loss: 0.3967 Epoch 2/50 45/45 [==============================] - 0s 913us/step - loss: 0.2189 Epoch 3/50 45/45 [==============================] - 0s 889us/step - loss: 0.1801 Epoch 4/50 45/45 [==============================] - 0s 888us/step - loss: 0.1613 Epoch 5/50 45/45 [==============================] - 0s 883us/step - loss: 0.1512 Epoch 6/50 45/45 [==============================] - 0s 878us/step - loss: 0.1448 Epoch 7/50 45/45 [==============================] - 0s 905us/step - loss: 0.1399 Epoch 8/50 45/45 [==============================] - 0s 937us/step - loss: 0.1374 Epoch 9/50 45/45 [==============================] - 0s 974us/step - loss: 0.1342 Epoch 10/50 45/45 [==============================] - 0s 979us/step - loss: 0.1318 Epoch 11/50 45/45 [==============================] - 0s 1ms/step - loss: 0.1307 Epoch 12/50 45/45 [==============================] - 0s 1ms/step - loss: 0.1071 Epoch 13/50 45/45 [==============================] - 0s 984us/step - loss: 0.0879 Epoch 14/50 45/45 [==============================] - 0s 980us/step - loss: 0.0861 Epoch 15/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0849 Epoch 16/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0844 Epoch 17/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0836 Epoch 18/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0824 Epoch 19/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0809 Epoch 20/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0818 Epoch 21/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0807 Epoch 22/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0799 Epoch 23/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0798 Epoch 24/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0788 Epoch 25/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0782 Epoch 26/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0772 Epoch 27/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0771 Epoch 28/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0769 Epoch 29/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0762 Epoch 30/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0753 Epoch 31/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0759 Epoch 32/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0751 Epoch 33/50 45/45 [==============================] - 0s 972us/step - loss: 0.0752 Epoch 34/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0753 Epoch 35/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0745 Epoch 36/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0739 Epoch 37/50 45/45 [==============================] - 0s 955us/step - loss: 0.0739 Epoch 38/50 45/45 [==============================] - 0s 985us/step - loss: 0.0738 Epoch 39/50 45/45 [==============================] - 0s 951us/step - loss: 0.0732 Epoch 40/50 45/45 [==============================] - 0s 928us/step - loss: 0.0726 Epoch 41/50 45/45 [==============================] - 0s 923us/step - loss: 0.0730 Epoch 42/50 45/45 [==============================] - 0s 925us/step - loss: 0.0732 Epoch 43/50 45/45 [==============================] - 0s 898us/step - loss: 0.0727 Epoch 44/50 45/45 [==============================] - 0s 926us/step - loss: 0.0719 Epoch 45/50 45/45 [==============================] - 0s 918us/step - loss: 0.0723 Epoch 46/50 45/45 [==============================] - 0s 942us/step - loss: 0.0713 Epoch 47/50 45/45 [==============================] - 0s 997us/step - loss: 0.0712 Epoch 48/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0707 Epoch 49/50 45/45 [==============================] - 0s 968us/step - loss: 0.0715 Epoch 50/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0715 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 946us/step - loss: 0.0711 Epoch 2/50 45/45 [==============================] - 0s 930us/step - loss: 0.0706 Epoch 3/50 45/45 [==============================] - 0s 875us/step - loss: 0.0707 Epoch 4/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0711 Epoch 5/50 45/45 [==============================] - 0s 906us/step - loss: 0.0710 Epoch 6/50 45/45 [==============================] - 0s 932us/step - loss: 0.0710 Epoch 7/50 45/45 [==============================] - 0s 892us/step - loss: 0.0709 Epoch 8/50 45/45 [==============================] - 0s 881us/step - loss: 0.0709 Epoch 9/50 45/45 [==============================] - 0s 920us/step - loss: 0.0705 Epoch 10/50 45/45 [==============================] - 0s 938us/step - loss: 0.0699 Epoch 11/50 45/45 [==============================] - 0s 942us/step - loss: 0.0709 Epoch 12/50 45/45 [==============================] - 0s 972us/step - loss: 0.0697 Epoch 13/50 45/45 [==============================] - 0s 959us/step - loss: 0.0699 Epoch 14/50 45/45 [==============================] - 0s 991us/step - loss: 0.0701 Epoch 15/50 45/45 [==============================] - 0s 976us/step - loss: 0.0700 Epoch 16/50 45/45 [==============================] - 0s 978us/step - loss: 0.0705 Epoch 17/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0704 Epoch 18/50 45/45 [==============================] - 0s 996us/step - loss: 0.0703 Epoch 19/50 45/45 [==============================] - 0s 967us/step - loss: 0.0695 Epoch 20/50 45/45 [==============================] - 0s 960us/step - loss: 0.0706 Epoch 21/50 45/45 [==============================] - 0s 968us/step - loss: 0.0703 Epoch 22/50 45/45 [==============================] - 0s 964us/step - loss: 0.0701 Epoch 23/50 45/45 [==============================] - 0s 952us/step - loss: 0.0708 Epoch 24/50 45/45 [==============================] - 0s 988us/step - loss: 0.0703 Epoch 25/50 45/45 [==============================] - 0s 991us/step - loss: 0.0704 Epoch 26/50 45/45 [==============================] - 0s 956us/step - loss: 0.0700 Epoch 27/50 45/45 [==============================] - 0s 965us/step - loss: 0.0705 Epoch 28/50 45/45 [==============================] - 0s 983us/step - loss: 0.0705 Epoch 29/50 45/45 [==============================] - 0s 966us/step - loss: 0.0703 Epoch 00029: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 940us/step - loss: 0.0704 Epoch 2/50 45/45 [==============================] - 0s 934us/step - loss: 0.0701 Epoch 3/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0702 Epoch 4/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0706 Epoch 5/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0706 Epoch 6/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0705 Epoch 7/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0706 Epoch 8/50 45/45 [==============================] - 0s 997us/step - loss: 0.0706 Epoch 9/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0701 Epoch 10/50 45/45 [==============================] - 0s 953us/step - loss: 0.0696 Epoch 11/50 45/45 [==============================] - 0s 904us/step - loss: 0.0706 Epoch 12/50 45/45 [==============================] - 0s 887us/step - loss: 0.0693 Epoch 13/50 45/45 [==============================] - 0s 869us/step - loss: 0.0697 Epoch 14/50 45/45 [==============================] - 0s 874us/step - loss: 0.0698 Epoch 15/50 45/45 [==============================] - 0s 867us/step - loss: 0.0697 Epoch 16/50 45/45 [==============================] - 0s 900us/step - loss: 0.0703 Epoch 17/50 45/45 [==============================] - 0s 865us/step - loss: 0.0701 Epoch 18/50 45/45 [==============================] - 0s 874us/step - loss: 0.0701 Epoch 19/50 45/45 [==============================] - 0s 879us/step - loss: 0.0693 Epoch 20/50 45/45 [==============================] - 0s 881us/step - loss: 0.0704 Epoch 21/50 45/45 [==============================] - 0s 911us/step - loss: 0.0701 Epoch 22/50 45/45 [==============================] - 0s 965us/step - loss: 0.0700 Epoch 00022: early stopping The 2th layer has been pretrained. Copying layer-wise pretrained weights to deep autoencoders Fine-tuning autoencoder end-to-end learning rate = 1 Epoch 1/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3707 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3694 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3686 Epoch 4/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3680 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3674 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3669 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3664 Epoch 8/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3660 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3656 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3652 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3648 Epoch 12/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3644 Epoch 13/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3640 Epoch 14/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3637 Epoch 15/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3634 Epoch 16/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3630 Epoch 17/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3627 Epoch 18/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3624 Epoch 19/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3621 Epoch 20/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3619 Epoch 21/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3616 Epoch 22/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3613 Epoch 23/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3611 Epoch 24/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3608 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3606 Epoch 26/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3603 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3601 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3599 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3596 Epoch 30/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3594 Epoch 31/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3592 Epoch 32/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3590 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3588 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3586 Epoch 35/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3584 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3582 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3580 Epoch 38/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3579 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3577 Epoch 40/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3575 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3573 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3572 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3570 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3568 Epoch 45/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3567 Epoch 46/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3565 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3564 Epoch 48/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3562 Epoch 49/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3561 Epoch 50/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3559 learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3555 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3554 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3554 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3554 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 8/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3553 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3553 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3553 Epoch 11/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3553 Epoch 12/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3552 Epoch 13/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3552 Epoch 14/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3552 Epoch 15/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3552 Epoch 16/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3552 Epoch 17/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3552 Epoch 18/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3552 Epoch 19/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3551 Epoch 20/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3551 Epoch 21/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3551 Epoch 22/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3551 Epoch 23/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3551 Epoch 24/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3551 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3551 Epoch 26/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 30/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3550 Epoch 31/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3550 Epoch 32/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 35/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3549 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 38/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 40/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 45/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 46/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 48/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 49/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 50/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 00011: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 00011: early stopping learning rate = 0.0001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 00011: early stopping learning rate = 1e-05 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 00011: early stopping Pretraining time is 78.82858276367188 Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:12)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 6 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.01627231946521242 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0628 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0462 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0385 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0328 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0283 The value of delta_label of current 2 th iteration is 0.029905884422552556 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1122 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0890 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0722 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0597 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0502 The value of delta_label of current 3 th iteration is 0.022605330284105902 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1294 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1037 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0858 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0732 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0640 The value of delta_label of current 4 th iteration is 0.013017855572169936 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1307 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1085 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0937 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0832 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0755 The value of delta_label of current 5 th iteration is 0.008883806843170024 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1219 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1086 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0991 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0920 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0863 The value of delta_label of current 6 th iteration is 0.007036678687659424 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1107 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1040 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0988 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0945 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0907 The value of delta_label of current 7 th iteration is 0.004573841146978626 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1026 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0987 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0953 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0924 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0898 The value of delta_label of current 8 th iteration is 0.003606297827425455 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0967 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0940 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0916 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0895 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0875 The value of delta_label of current 9 th iteration is 0.002023045122702085 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0922 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0902 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0884 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0867 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0852 The value of delta_label of current 10 th iteration is 0.0019350866391063418 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0887 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0871 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0857 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0843 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0831 The value of delta_label of current 11 th iteration is 0.001759169671914856 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0858 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0846 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0834 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0823 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0812 The value of delta_label of current 12 th iteration is 0.0014952942211276278 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0835 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0824 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0814 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0804 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0795 The value of delta_label of current 13 th iteration is 0.0021110036062978272 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0816 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0806 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0797 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0789 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0781 delta_label 0.0009675433195531709 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 4964 1 2455 2 2454 3 776 4 548 5 172 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_2" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 6) 192 ================================================================= Total params: 277,344 Trainable params: 277,344 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.1)is: 104.78796601295471
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne0.1 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.1 into the umap coordinates (adata.obsm)
The run time for all resolution is: 136.38761711120605
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.016122102737426758
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 9 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.03465564253672267 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0789 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0624 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0538 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0470 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0414 The value of delta_label of current 2 th iteration is 0.019614741841850646 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1356 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1126 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0948 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0811 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0704 The value of delta_label of current 3 th iteration is 0.013193772539361421 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1627 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1389 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1199 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1051 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0936 The value of delta_label of current 4 th iteration is 0.010906851965872108 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1780 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1553 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1378 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1246 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1143 The value of delta_label of current 5 th iteration is 0.012490104670595479 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1837 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1666 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1535 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1433 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1351 The value of delta_label of current 6 th iteration is 0.010818893482276366 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1804 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1696 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1608 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1535 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1473 The value of delta_label of current 7 th iteration is 0.011698478318233793 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1738 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1665 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1603 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1550 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1503 The value of delta_label of current 8 th iteration is 0.011610519834638051 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1680 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1626 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1579 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1538 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1501 The value of delta_label of current 9 th iteration is 0.011082768933063593 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1640 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1596 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1557 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1524 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1493 The value of delta_label of current 10 th iteration is 0.009763391679127452 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1612 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1574 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1540 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1510 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1483 The value of delta_label of current 11 th iteration is 0.009147682293957252 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1588 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1554 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1523 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1496 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1470 The value of delta_label of current 12 th iteration is 0.006684844753276454 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1564 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1533 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1504 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1479 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1456 The value of delta_label of current 13 th iteration is 0.005101592048553083 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1537 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1508 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1483 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1461 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1439 The value of delta_label of current 14 th iteration is 0.0034303808602339694 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1507 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1482 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1459 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1439 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1420 The value of delta_label of current 15 th iteration is 0.0021110036062978272 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1474 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1453 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1433 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1416 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1399 The value of delta_label of current 16 th iteration is 0.0015832527047233706 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1442 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1423 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1406 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1391 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1376 The value of delta_label of current 17 th iteration is 0.001407335737531885 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1411 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1395 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1380 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1367 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1354 delta_label 0.0009675433195531709 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is: 0 3383 1 2129 2 1575 3 1619 4 773 5 419 6 317 7 147 8 1007 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_3" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 9) 288 ================================================================= Total params: 277,440 Trainable params: 277,440 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.2)is: 16.52006721496582
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.2 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.2 into the umap coordinates (adata.obsm)
The run time for all resolution is: 47.07176899909973
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.017837047576904297
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 9 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.032456680446829096 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0789 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0624 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0539 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0470 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0414 The value of delta_label of current 2 th iteration is 0.01970270032544639 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1355 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1126 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0948 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0811 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0704 The value of delta_label of current 3 th iteration is 0.012578063154191221 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1624 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1387A: 0s - loss: 0.14 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1198 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1050 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0936 The value of delta_label of current 4 th iteration is 0.011434602867446565 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1775 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1549 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1375 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1244 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1141 The value of delta_label of current 5 th iteration is 0.012402146186999736 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1833 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1662 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1531 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1430 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1348 The value of delta_label of current 6 th iteration is 0.011962353769021022 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1805 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1696 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1607 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1534 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1472 The value of delta_label of current 7 th iteration is 0.011786436801829536 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1742 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1668 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1606 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1552 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1505 The value of delta_label of current 8 th iteration is 0.012050312252616765 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1685 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1630 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1583 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1542 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1504 The value of delta_label of current 9 th iteration is 0.01125868590025508 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1645 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1601 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1561 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1528 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1496 The value of delta_label of current 10 th iteration is 0.01064297651508488 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1617 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1578 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1544 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1514 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1486 The value of delta_label of current 11 th iteration is 0.008004222007212595 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1593 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1558 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1527 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1500 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1475 The value of delta_label of current 12 th iteration is 0.006508927786084968 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1568 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1536 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1508 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1483 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1460 The value of delta_label of current 13 th iteration is 0.005365467499340312 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1541 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1511 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1486 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1463 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1442 The value of delta_label of current 14 th iteration is 0.0038701732782126835 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1511 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1484 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1462 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1442 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1423 The value of delta_label of current 15 th iteration is 0.00219896208989357 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1479 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1456 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1437 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1419 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1402 The value of delta_label of current 16 th iteration is 0.0015832527047233706 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1446 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1427 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1411 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1395 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1380 The value of delta_label of current 17 th iteration is 0.0015832527047233706 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1415 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1399 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1384 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1371 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1358 delta_label 0.000439792417978714 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 3358 1 2129 2 1577 3 1636 4 773 5 419 6 316 7 147 8 1014 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_4" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 9) 288 ================================================================= Total params: 277,440 Trainable params: 277,440 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.4)is: 16.41282367706299
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.4 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.4 into the umap coordinates (adata.obsm)
The run time for all resolution is: 47.394776821136475
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.013768911361694336
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 10 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06420969302489225 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0842 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0677 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0592 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0522 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0464 The value of delta_label of current 2 th iteration is 0.025507960242765415 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1465 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1233 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1050 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0905 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0788 The value of delta_label of current 3 th iteration is 0.01345764799014865 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1808 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1548 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1337 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1173 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1043 The value of delta_label of current 4 th iteration is 0.01222622921980825 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2038 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1779 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1582 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1433 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1318 The value of delta_label of current 5 th iteration is 0.010555018031489137 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2164 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1975 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1831 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1719 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1628 The value of delta_label of current 6 th iteration is 0.009147682293957252 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2167 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2048 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1949 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1866 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1795 The value of delta_label of current 7 th iteration is 0.007388512622042396 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2104 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2023 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1951 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1888 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1832 The value of delta_label of current 8 th iteration is 0.004485882663382883 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2030 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1969 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1912 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1863 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1818 The value of delta_label of current 9 th iteration is 0.0037822147946169407 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1958 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1909 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1863 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1822 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1784 The value of delta_label of current 10 th iteration is 0.0029026299586595128 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1891 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1850 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1812 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1777 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1745 The value of delta_label of current 11 th iteration is 0.0012314187703403993 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1828 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1794 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1762 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1733 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1706 The value of delta_label of current 12 th iteration is 0.001407335737531885 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1770 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1742 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1715 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1690 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1667 delta_label 0.0007916263523616853 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 2402 1 2081 2 2179 3 1578 4 1365 5 779 6 396 7 315 8 192 9 82 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_5" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 10) 320 ================================================================= Total params: 277,472 Trainable params: 277,472 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.6)is: 13.11959195137024
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.6 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.6 into the umap coordinates (adata.obsm)
The run time for all resolution is: 43.96219491958618
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.014747142791748047
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 11 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.052159380772275485 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0894 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0730 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0641 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0568 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0507 The value of delta_label of current 2 th iteration is 0.021110036062978274 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1482 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1251 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1071 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0931 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0821 The value of delta_label of current 3 th iteration is 0.010906851965872108 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1813 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1565 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1367 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1210 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1086 The value of delta_label of current 4 th iteration is 0.011082768933063593 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2061 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1810 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1621 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1479 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1368 The value of delta_label of current 5 th iteration is 0.008883806843170024 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2221 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2034 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1891 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1779 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1687 The value of delta_label of current 6 th iteration is 0.008531972908787053 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2239 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2119 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2020 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1936 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1864 The value of delta_label of current 7 th iteration is 0.0063330108188934826 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2186 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2101 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2027 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1961 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1902 The value of delta_label of current 8 th iteration is 0.005189550532148826 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2114 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2048 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1990 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1937 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1889 The value of delta_label of current 9 th iteration is 0.0031665054094467413 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2041 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1988 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1940 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1897 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1857 The value of delta_label of current 10 th iteration is 0.0024628375406807986 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1972 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1928 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1888 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1852 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1818 The value of delta_label of current 11 th iteration is 0.0015832527047233706 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1907 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1871 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1837 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1807 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1778 The value of delta_label of current 12 th iteration is 0.0013193772539361421 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1848 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1817 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1790 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1764 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1739 The value of delta_label of current 13 th iteration is 0.0010555018031489136 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1794 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1768 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1745 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1723 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1702 delta_label 0.0006157093851701996 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 2487 1 2235 2 2137 3 1576 4 1252 5 446 6 393 7 331 8 318 9 138 10 56 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_6" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 11) 352 ================================================================= Total params: 277,504 Trainable params: 277,504 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.8)is: 13.096119165420532
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.8 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8 into the umap coordinates (adata.obsm)
The run time for all resolution is: 43.638885736465454
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.014670133590698242
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 13 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.06711232298355177 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0996 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0831 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0737 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0660 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0594 The value of delta_label of current 2 th iteration is 0.03632685372504178 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1611 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1407 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1239 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1101 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0988 The value of delta_label of current 3 th iteration is 0.03131322016008444 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1978 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1753 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1568 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1418 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1296 The value of delta_label of current 4 th iteration is 0.031137303192892953 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2302 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2054 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1866 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1721 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1608 The value of delta_label of current 5 th iteration is 0.023836749054446302 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2515 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2322 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2176 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2060 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1965 The value of delta_label of current 6 th iteration is 0.017679655202744303 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2582 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2451 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2345 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2254 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2176 The value of delta_label of current 7 th iteration is 0.01064297651508488 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2574 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2478 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2397 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2324 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2260 The value of delta_label of current 8 th iteration is 0.008619931392382795 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2533 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2459 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2393 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2331 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2276 The value of delta_label of current 9 th iteration is 0.0047497581141701115 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2480 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2416 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2358 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2303 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2254 The value of delta_label of current 10 th iteration is 0.0038701732782126835 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2422 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2367 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2318 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2270 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2228 The value of delta_label of current 11 th iteration is 0.0030785469258509984 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2361 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2314 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2271 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2230 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2193 The value of delta_label of current 12 th iteration is 0.00219896208989357 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2298 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2257 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2220 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2185 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2153 The value of delta_label of current 13 th iteration is 0.0010555018031489136 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2237 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2202 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2171 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2141 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2113 delta_label 0.0007916263523616853 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 2364 1 2153 2 1564 3 1259 4 467 5 962 6 444 7 390 8 1012 9 333 10 278 11 96 12 47 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_7" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 13) 416 ================================================================= Total params: 277,568 Trainable params: 277,568 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.0)is: 13.499810934066772
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne1.0 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.0 into the umap coordinates (adata.obsm)
The run time for all resolution is: 44.50366282463074
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.018655061721801758
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 13 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.06632069663119008 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0996 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0831 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0738 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0661 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0595 The value of delta_label of current 2 th iteration is 0.03606297827425455 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1608 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1406 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1238 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1101 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0987 The value of delta_label of current 3 th iteration is 0.029817925938956814 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1976 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1749 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1563 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1412 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1291 The value of delta_label of current 4 th iteration is 0.031840971061658896 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2303 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2052 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1863 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1718 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1605 The value of delta_label of current 5 th iteration is 0.024892250857595215 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2516 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2322 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2176 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2060 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1965 The value of delta_label of current 6 th iteration is 0.015744568563637963 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2580 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2449 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2343 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2252 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2174 The value of delta_label of current 7 th iteration is 0.011170727416659337 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2569 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2475 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2395 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2321 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2258 The value of delta_label of current 8 th iteration is 0.007652388072829625 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2529 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2455 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2390 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2329 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2274 The value of delta_label of current 9 th iteration is 0.00562934295012754 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2476 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2413 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2356 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2302 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2252 The value of delta_label of current 10 th iteration is 0.00439792417978714 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2418 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2363 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2314 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2267 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2224 The value of delta_label of current 11 th iteration is 0.0034303808602339694 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2358 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2311 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2269 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2228 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2190 The value of delta_label of current 12 th iteration is 0.002023045122702085 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2296 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2256 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2219 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2183 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2150 The value of delta_label of current 13 th iteration is 0.001759169671914856 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2236 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2201 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2169 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2139 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2110 The value of delta_label of current 14 th iteration is 0.0011434602867446565 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2179 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2149 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2121 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2096 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2071 delta_label 0.0002638754507872284 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 2357 1 2163 2 1564 3 1258 4 464 5 963 6 444 7 390 8 1017 9 333 10 278 11 42 12 96 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_8" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 13) 416 ================================================================= Total params: 277,568 Trainable params: 277,568 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.2)is: 14.362415790557861
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:31)
computing neighbors
tsne finished and added X_tsne1.2 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.2 into the umap coordinates (adata.obsm)
The run time for all resolution is: 46.85865616798401
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.016456127166748047
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 15 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.07590817134312604 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1028 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0867 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0775 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0701 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0638 The value of delta_label of current 2 th iteration is 0.04116457032280763 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1653 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1461 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1301 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1168 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1057 The value of delta_label of current 3 th iteration is 0.03606297827425455 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2046 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1822 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1640 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1495 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1377 The value of delta_label of current 4 th iteration is 0.03773418946257367 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2424 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2182 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1997 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1854 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1741 The value of delta_label of current 5 th iteration is 0.029905884422552556 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2701 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2508 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2360 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2242 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2144 The value of delta_label of current 6 th iteration is 0.02251737180051016 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2805 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2671 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2562 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2470 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2389 The value of delta_label of current 7 th iteration is 0.014864983727680536 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2824 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2725 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2639 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2564 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2496 The value of delta_label of current 8 th iteration is 0.009323599261148738 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2810 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2732 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2661 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2598 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 The value of delta_label of current 9 th iteration is 0.010115225613510423 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2781 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2715 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2655 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2599 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2548 The value of delta_label of current 10 th iteration is 0.006772803236872196 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2744 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2687 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2633 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2538 The value of delta_label of current 11 th iteration is 0.0058052599173190255 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2702 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2651 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2603 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2559 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2517 The value of delta_label of current 12 th iteration is 0.003958131761808426 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2655 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2610 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2566 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2526 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2488 The value of delta_label of current 13 th iteration is 0.0029905884422552556 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2604 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2564 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2525 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2454 The value of delta_label of current 14 th iteration is 0.003342422376638227 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2516 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2481 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2449 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2417 The value of delta_label of current 15 th iteration is 0.002023045122702085 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2500 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2469 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2437 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2408 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2379 The value of delta_label of current 16 th iteration is 0.0014952942211276278 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2450 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2421 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2392 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2366 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2340 delta_label 0.0009675433195531709 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is: 0 2349 1 1666 2 1563 3 1168 4 352 5 884 6 444 7 388 8 978 9 334 10 283 11 47 12 94 13 162 14 657 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_9" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 15) 480 ================================================================= Total params: 277,632 Trainable params: 277,632 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.4)is: 17.228896141052246
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.4 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.4 into the umap coordinates (adata.obsm)
The run time for all resolution is: 48.980205059051514
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.01580333709716797
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 17 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.10255959187263612 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1060 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0897 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0807 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0733 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0670 The value of delta_label of current 2 th iteration is 0.05602955405048817 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1711 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1519 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1359 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1227 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1115 The value of delta_label of current 3 th iteration is 0.04565045298619052 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2100 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1889 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1716 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1574 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1455 The value of delta_label of current 4 th iteration is 0.043275573929105464 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2445 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2229 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2060 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1928 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1820 The value of delta_label of current 5 th iteration is 0.03703052159380772 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2727 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2549 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2409 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2297 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2202 The value of delta_label of current 6 th iteration is 0.033776057700765236 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2874 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2741 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2632 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2459 The value of delta_label of current 7 th iteration is 0.026563462045914327 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2929 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2827 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2739 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2662 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2592 The value of delta_label of current 8 th iteration is 0.01917494942387193 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2940 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2857 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2784 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2716 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2654 The value of delta_label of current 9 th iteration is 0.016975987333978364 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2928 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2856 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2792 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2733 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2678 The value of delta_label of current 10 th iteration is 0.015568651596446477 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2902 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2840 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2783 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2730 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2681 The value of delta_label of current 11 th iteration is 0.011346644383850822 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2871 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2816 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2765 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2717 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2673 The value of delta_label of current 12 th iteration is 0.00905972381036151 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2843 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2792 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2746 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2702 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2662 The value of delta_label of current 13 th iteration is 0.0050136335649573404 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2819 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2772 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2730 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2689 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2653 The value of delta_label of current 14 th iteration is 0.003606297827425455 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2795 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2752 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2713 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2675 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2642 The value of delta_label of current 15 th iteration is 0.0025507960242765414 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2768 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2728 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2692 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2658 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2627 The value of delta_label of current 16 th iteration is 0.001847128155510599 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2734 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2698 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2666 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2634 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2606 The value of delta_label of current 17 th iteration is 0.0021110036062978272 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2696 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2663 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2634 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2606 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2580 The value of delta_label of current 18 th iteration is 0.0013193772539361421 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2655 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2625 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2600 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2574 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2550 delta_label 0.0002638754507872284 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is: 0 2170 1 1272 2 1149 3 1231 4 418 5 895 6 1132 7 445 8 386 9 996 10 334 11 285 12 359 13 27 14 173 15 82 16 15 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_10" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 17) 544 ================================================================= Total params: 277,696 Trainable params: 277,696 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.6)is: 19.20682692527771
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.6 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.6 into the umap coordinates (adata.obsm)
The run time for all resolution is: 51.01515197753906
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.012847185134887695
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 20 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.1493535051455713 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1115 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0957 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0870 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0797 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0735 The value of delta_label of current 2 th iteration is 0.07370920925323247 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1770 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1593 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1441 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1312 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1201 The value of delta_label of current 3 th iteration is 0.055237927698126486 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2174 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1973 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1808 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1673 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1560 The value of delta_label of current 4 th iteration is 0.052687131673849946 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2348 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2184 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2052 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1946 The value of delta_label of current 5 th iteration is 0.060075644295892336 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2857 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2688 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2437 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2343 The value of delta_label of current 6 th iteration is 0.057524848271615796 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3016 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2888 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2780 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2686 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2605 The value of delta_label of current 7 th iteration is 0.04653003782214794 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3073 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2972 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2884 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2804 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2732 The value of delta_label of current 8 th iteration is 0.031577095610871665 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3075 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2991 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2915 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2845 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2781 The value of delta_label of current 9 th iteration is 0.024276541472425014 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3047 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2974 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2910 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2848 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2793 The value of delta_label of current 10 th iteration is 0.021725745448148474 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3001 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2939 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2883 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2828 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2780 The value of delta_label of current 11 th iteration is 0.01996657577623362 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2948 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2893 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2844 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2796 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2753 The value of delta_label of current 12 th iteration is 0.021813703931744217 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2891 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2844 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2801 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2759 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2721 The value of delta_label of current 13 th iteration is 0.01882311548948896 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2836 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2795 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2757 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2720 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2686 The value of delta_label of current 14 th iteration is 0.016360277948808163 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2785 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2748 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2714 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2682 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2652 The value of delta_label of current 15 th iteration is 0.017415779751957076 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2738 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2705 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2676 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2647 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2621 The value of delta_label of current 16 th iteration is 0.015392734629254992 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2696 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2667 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2641 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2616 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2592 The value of delta_label of current 17 th iteration is 0.013985398891723106 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2660 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2634 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2610 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2588 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2566 The value of delta_label of current 18 th iteration is 0.01345764799014865 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2629 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2606 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2564 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2544 The value of delta_label of current 19 th iteration is 0.012666021637786965 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2602 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2562 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2543 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2525 The value of delta_label of current 20 th iteration is 0.01187439528542528 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2579 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2561 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2543 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2525 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2509 The value of delta_label of current 21 th iteration is 0.012402146186999736 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2560 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2543 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2526 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2511 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2496 The value of delta_label of current 22 th iteration is 0.01222622921980825 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2544 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2528 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2513 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2498 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2484 The value of delta_label of current 23 th iteration is 0.009587474711935965 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2517 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2502 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2476 The value of delta_label of current 24 th iteration is 0.009323599261148738 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2523 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2508 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2495 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2470 The value of delta_label of current 25 th iteration is 0.00782830504002111 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2517 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2504 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2490 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2478 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 The value of delta_label of current 26 th iteration is 0.007388512622042396 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2515 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2501 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 The value of delta_label of current 27 th iteration is 0.0063330108188934826 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2514 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2501 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 The value of delta_label of current 28 th iteration is 0.005717301433723282 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2513 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2500 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2488 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2467 The value of delta_label of current 29 th iteration is 0.0047497581141701115 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2511 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2499 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2487 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2476 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 The value of delta_label of current 30 th iteration is 0.0031665054094467413 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2507 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2495 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2484 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2473 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2463 The value of delta_label of current 31 th iteration is 0.003606297827425455 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2501 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2490 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2479 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2468 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2458 The value of delta_label of current 32 th iteration is 0.0021110036062978272 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2493 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2471 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2461 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2451 The value of delta_label of current 33 th iteration is 0.00219896208989357 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2472 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2461 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2451 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2442 The value of delta_label of current 34 th iteration is 0.0023748790570850557 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2469 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2459 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2449 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2440 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2431 The value of delta_label of current 35 th iteration is 0.0016712111883191135 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2454 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2445 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2435 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2427 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2418 The value of delta_label of current 36 th iteration is 0.001407335737531885 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2438 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2430 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2421 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2413 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2405 The value of delta_label of current 37 th iteration is 0.0014952942211276278 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2422 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2414 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2406 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2398 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2391 The value of delta_label of current 38 th iteration is 0.0014952942211276278 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2406 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2398 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2391 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2384 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2377 The value of delta_label of current 39 th iteration is 0.0031665054094467413 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2390 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2383 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2377 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2370 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2364 The value of delta_label of current 40 th iteration is 0.0034303808602339694 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2375 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2369 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2363 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2357 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2352 The value of delta_label of current 41 th iteration is 0.003958131761808426 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2361 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2355 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2350 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2344 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2339 The value of delta_label of current 42 th iteration is 0.004309965696191398 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2348 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2342 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2337 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2332 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2327 The value of delta_label of current 43 th iteration is 0.003694256311021198 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2335 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2330 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2325 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2320 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2316 The value of delta_label of current 44 th iteration is 0.002286920573489313 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2322 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2318 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2313 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2309 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2304 The value of delta_label of current 45 th iteration is 0.002726712991468027 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2310 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2306 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2302 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2297 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2293 The value of delta_label of current 46 th iteration is 0.003342422376638227 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2299 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2295 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2290 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2286 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2282 The value of delta_label of current 47 th iteration is 0.002023045122702085 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2287 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2283 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2279 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2275 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2271 The value of delta_label of current 48 th iteration is 0.002286920573489313 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2276 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2272 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2269 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2265 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2261 The value of delta_label of current 49 th iteration is 0.00219896208989357 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2265 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2262 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2258 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2254 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2251 The value of delta_label of current 50 th iteration is 0.0029905884422552556 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2255 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2252 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2248 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2245 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2242 The value of delta_label of current 51 th iteration is 0.00439792417978714 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2245 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2242 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2239 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2236 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2233 The value of delta_label of current 52 th iteration is 0.008883806843170024 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2236 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2233 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2230 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2227 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2224 The value of delta_label of current 53 th iteration is 0.008180138974404082 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2227 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2224 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2222 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2219 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2216 The value of delta_label of current 54 th iteration is 0.013809481924531622 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2219 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2216 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2213 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2211 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2208 The value of delta_label of current 55 th iteration is 0.017063945817574106 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2210 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2208 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2205 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2203 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2200 The value of delta_label of current 56 th iteration is 0.024892250857595215 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2202 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2200 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2198 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2195 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2192 The value of delta_label of current 57 th iteration is 0.028234673234233443 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2195 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2192 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2190 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2187 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2185 The value of delta_label of current 58 th iteration is 0.035007476471105636 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2187 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2185 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2182 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2180 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2178 The value of delta_label of current 59 th iteration is 0.03386401618436098 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2179 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2177 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2175 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2173 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2171 The value of delta_label of current 60 th iteration is 0.03465564253672267 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2172 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2170 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2168 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2166 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2164 The value of delta_label of current 61 th iteration is 0.027970797783446213 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2165 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2163 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2161 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2159 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2157 The value of delta_label of current 62 th iteration is 0.020494326677808074 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2158 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2157 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2155 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2153 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2150 The value of delta_label of current 63 th iteration is 0.018031489137127276 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2152 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2150 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2148 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2146 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2144 The value of delta_label of current 64 th iteration is 0.02128595303016976 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2145 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2144 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2142 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2140 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2138 The value of delta_label of current 65 th iteration is 0.017327821268361333 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2139 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2138 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2136 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2134 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2132 The value of delta_label of current 66 th iteration is 0.00782830504002111 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2133 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2132 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2130 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2128 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2127 The value of delta_label of current 67 th iteration is 0.007740346556425367 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2128 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2126 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2125 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2123 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2121 The value of delta_label of current 68 th iteration is 0.004573841146978626 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2122 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2121 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2119 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2118 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2116 delta_label 0.0 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 2234 1 857 2 1206 3 1251 4 1464 5 799 6 466 7 346 8 445 9 17 10 381 11 634 12 333 13 378 14 281 15 23 16 156 17 83 18 15 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_11" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 20) 640 ================================================================= Total params: 277,792 Trainable params: 277,792 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.8)is: 66.3656268119812
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:32)
computing neighbors
tsne finished and added X_tsne1.8 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.8 into the umap coordinates (adata.obsm)
The run time for all resolution is: 99.36555004119873
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8'
obsp: 'distances', 'connectivities'
Start to process resolution= 2.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.014740943908691406
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 24 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.19905004837716597 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1131 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0982 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0899 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0831 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0772 The value of delta_label of current 2 th iteration is 0.08039405400650892 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1790 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1629 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1491 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1372 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1272 The value of delta_label of current 3 th iteration is 0.06139502154982848 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2189 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2021 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1876 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1754 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1650 The value of delta_label of current 4 th iteration is 0.05866830855836045 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2362 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2214 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2093 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1992 The value of delta_label of current 5 th iteration is 0.06693640601636028 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2847 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2687 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2557 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2450 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2358 The value of delta_label of current 6 th iteration is 0.06605682118040285 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3044 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2918 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2813 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2723 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2643 The value of delta_label of current 7 th iteration is 0.052071422288679746 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3156 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3055 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2966 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2888 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2817 The value of delta_label of current 8 th iteration is 0.048992875362828744 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3218 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3131 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3054 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2984 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2920 The value of delta_label of current 9 th iteration is 0.046178203887764974 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3248 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3172 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3104 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3040 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2982 The value of delta_label of current 10 th iteration is 0.035007476471105636 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3256 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3188 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3127 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3069 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3015 The value of delta_label of current 11 th iteration is 0.030345676840531268 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3250 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3189 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3134 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3081 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3032 The value of delta_label of current 12 th iteration is 0.024804292373999472 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3235 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3180 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3131 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3084 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3039 The value of delta_label of current 13 th iteration is 0.02533204327557393 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3214 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3165 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3120 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3078 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3037 The value of delta_label of current 14 th iteration is 0.022165537866127186 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3191 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3146 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3105 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3067 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3029 The value of delta_label of current 15 th iteration is 0.020494326677808074 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3166 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3126 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3088 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3053 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3019 The value of delta_label of current 16 th iteration is 0.01600844401442519 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3143 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3106 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3071 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3039 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3008 The value of delta_label of current 17 th iteration is 0.013017855572169936 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3121 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3087 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3055 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3026 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2996 The value of delta_label of current 18 th iteration is 0.012578063154191221 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3101 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3070 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3040 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3013 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2986 The value of delta_label of current 19 th iteration is 0.011786436801829536 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3081 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3053 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3026 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3001 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2975 The value of delta_label of current 20 th iteration is 0.010467059547893395 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3062 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3036 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3011 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2988 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2963 The value of delta_label of current 21 th iteration is 0.011786436801829536 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3041 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3017 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2994 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2972 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2949 The value of delta_label of current 22 th iteration is 0.008268097457999824 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3019 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2997 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2975 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2955 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2934 The value of delta_label of current 23 th iteration is 0.007300554138446653 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2996 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2976 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2955 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2937 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2917 The value of delta_label of current 24 th iteration is 0.007740346556425367 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2972 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2953 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2934 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2918 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2899 The value of delta_label of current 25 th iteration is 0.0058052599173190255 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2948 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2931 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2913 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2898 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2880 The value of delta_label of current 26 th iteration is 0.004925675081361597 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2924 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2908 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2892 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2878 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2862 The value of delta_label of current 27 th iteration is 0.0047497581141701115 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2901 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2886 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2871 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2858 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2844 The value of delta_label of current 28 th iteration is 0.00562934295012754 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2878 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2865 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2851 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2839 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2826 The value of delta_label of current 29 th iteration is 0.003254463893042484 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2857 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2844 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2831 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2820 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2808 The value of delta_label of current 30 th iteration is 0.0037822147946169407 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2836 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2824 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2812 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2802 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2791 The value of delta_label of current 31 th iteration is 0.003342422376638227 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2816 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2805 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2794 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2785 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2775 The value of delta_label of current 32 th iteration is 0.002726712991468027 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2798 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2788 Epoch 3/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2778 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2769 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2759 The value of delta_label of current 33 th iteration is 0.0025507960242765414 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2781 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2772 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2762 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2754 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2745 The value of delta_label of current 34 th iteration is 0.0024628375406807986 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2766 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2757 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2747 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2739 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2731 The value of delta_label of current 35 th iteration is 0.001847128155510599 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2751 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2743 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2734 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2726 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2718 The value of delta_label of current 36 th iteration is 0.002023045122702085 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2738 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2729 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2721 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2714 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2707 The value of delta_label of current 37 th iteration is 0.001759169671914856 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2725 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2717 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2710 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2703 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2696 The value of delta_label of current 38 th iteration is 0.0029905884422552556 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2713 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2705 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2698 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2692 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2685 The value of delta_label of current 39 th iteration is 0.0021110036062978272 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2701 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2694 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2687 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2681 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2675 The value of delta_label of current 40 th iteration is 0.0023748790570850557 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2690 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2683 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2676 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2670 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2664 The value of delta_label of current 41 th iteration is 0.002726712991468027 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2679 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2672 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2666 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2660 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2654 The value of delta_label of current 42 th iteration is 0.001759169671914856 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2668 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2661 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2655 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2650 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2644 The value of delta_label of current 43 th iteration is 0.003254463893042484 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2657 Epoch 2/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2651 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2645 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2640 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2635 The value of delta_label of current 44 th iteration is 0.003518339343829712 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2646 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2640 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2635 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2630 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2625 The value of delta_label of current 45 th iteration is 0.003254463893042484 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2635 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2630 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2625 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2620 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2615 The value of delta_label of current 46 th iteration is 0.0031665054094467413 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2625 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2620 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2615 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2610 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2606 The value of delta_label of current 47 th iteration is 0.003518339343829712 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2614 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2610 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2605 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2601 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2596 The value of delta_label of current 48 th iteration is 0.0034303808602339694 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2604 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2600 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2595 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2591 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2587 The value of delta_label of current 49 th iteration is 0.0058052599173190255 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2594 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2590 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2586 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2578 The value of delta_label of current 50 th iteration is 0.007124637171255168 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2580 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2576 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2573 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2569 The value of delta_label of current 51 th iteration is 0.010115225613510423 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2575 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2571 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2567 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2564 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2560 The value of delta_label of current 52 th iteration is 0.014337232826106078 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2566 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2562 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2558 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2555 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 The value of delta_label of current 53 th iteration is 0.019262907907467677 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2556 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2553 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2549 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2546 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2543 The value of delta_label of current 54 th iteration is 0.02911425807019087 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2547 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2544 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2541 Epoch 4/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2538 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2534 The value of delta_label of current 55 th iteration is 0.031137303192892953 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2538 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2535 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2529 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2526 The value of delta_label of current 56 th iteration is 0.03043363532412701 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2530 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2527 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2524 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2521 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2518 The value of delta_label of current 57 th iteration is 0.02972996745536107 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2522 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2519 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2516 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2513 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2510 The value of delta_label of current 58 th iteration is 0.029554050488169583 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2514 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2511 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2508 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2506 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2503 The value of delta_label of current 59 th iteration is 0.022077579382531444 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2506 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2504 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2501 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2498 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2496 The value of delta_label of current 60 th iteration is 0.021461869997361247 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2499 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2496 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2494 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2491 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 The value of delta_label of current 61 th iteration is 0.021637786964552732 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2491 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2487 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2484 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 The value of delta_label of current 62 th iteration is 0.025507960242765415 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2484 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2480 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2475 The value of delta_label of current 63 th iteration is 0.029817925938956814 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2475 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2473 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2471 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2469 The value of delta_label of current 64 th iteration is 0.025947752660744127 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2471 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2469 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2464 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2462 The value of delta_label of current 65 th iteration is 0.024188582988829272 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2464 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2463 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2461 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2458 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2456 The value of delta_label of current 66 th iteration is 0.025420001759169673 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2458 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2456 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2454 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2452 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2450 The value of delta_label of current 67 th iteration is 0.02665142052951007 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2452 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2450 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2448 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2446 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2444 The value of delta_label of current 68 th iteration is 0.01759169671914856 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2445 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2443 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2442 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2440 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2438 The value of delta_label of current 69 th iteration is 0.003958131761808426 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2440 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2438 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2436 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2434 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2432 The value of delta_label of current 70 th iteration is 0.0030785469258509984 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2434 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2432 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2430 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2428 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2426 The value of delta_label of current 71 th iteration is 0.0030785469258509984 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2428 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2426 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2425 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2423 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2421 The value of delta_label of current 72 th iteration is 0.0037822147946169407 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2422 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2421 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2419 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2417 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2416 The value of delta_label of current 73 th iteration is 0.0029905884422552556 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2417 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2416 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2414 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2412 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2410 The value of delta_label of current 74 th iteration is 0.0026387545078722843 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2412 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2410 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2409 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2407 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2405 The value of delta_label of current 75 th iteration is 0.0037822147946169407 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2407 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2405 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2404 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2402 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2400 The value of delta_label of current 76 th iteration is 0.002286920573489313 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2402 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2400 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2399 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2397 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2395 delta_label 0.0 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
The final prediction cluster is: 0 1775 1 1285 2 1815 3 1102 4 621 5 303 6 306 7 445 8 21 9 501 10 379 11 783 12 303 13 332 14 277 15 512 16 366 17 19 18 83 19 118 20 8 21 15 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_12" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 24) 768 ================================================================= Total params: 277,920 Trainable params: 277,920 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=2.0)is: 74.8167040348053
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:31)
computing neighbors
tsne finished and added X_tsne2.0 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap2.0 into the umap coordinates (adata.obsm)
The run time for all resolution is: 107.1918740272522
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8', 'desc_2.0'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8', 'prob_matrix2.0'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8', 'X_Embeded_z2.0', 'X_tsne2.0', 'X_umap2.0'
obsp: 'distances', 'connectivities'
total_clusters
[6, 9, 9, 10, 11, 13, 13, 15, 17, 19, 22]
#go back and pick a resolution in the middle (0.8) to highlight
adata = desc.train(adata, dims=[adata.shape[1], 128, 32], tol=0.001, n_neighbors=10,
batch_size=256, louvain_resolution=0.8, do_tsne=True, learning_rate=300,
do_umap=True, num_Cores_tsne=4)
Start to process resolution= 0.8 The number of cpu in your computer is 12 Create the directory:result_tmp to save result Checking whether result_tmp/ae_weights.h5 exists in the directory The file ae_weights.h5 is not exits Pretraining the 1th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 1s 7ms/step - loss: 0.5051 Epoch 2/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4777 Epoch 3/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4559 Epoch 4/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4424 Epoch 5/50 45/45 [==============================] - 0s 9ms/step - loss: 0.4326 Epoch 6/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4241 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.4169 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4113 Epoch 9/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4064 Epoch 10/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4030 Epoch 11/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4000 Epoch 12/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3976 Epoch 13/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3955 Epoch 14/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3938 Epoch 15/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3924 Epoch 16/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3911 Epoch 17/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3900 Epoch 18/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3891 Epoch 19/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3882 Epoch 20/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3873 Epoch 21/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3866 Epoch 22/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3859 Epoch 23/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3852 Epoch 24/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3846 Epoch 25/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3842 Epoch 26/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3835 Epoch 27/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3830 Epoch 28/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3825 Epoch 29/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3819 Epoch 30/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3815 Epoch 31/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3810 Epoch 32/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3806 Epoch 33/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3800 Epoch 34/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3797 Epoch 35/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3792 Epoch 36/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3788 Epoch 37/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3784 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3782 Epoch 39/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3777 Epoch 40/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3773 Epoch 41/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3770 Epoch 42/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3767 Epoch 43/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3763 Epoch 44/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3761 Epoch 45/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3758 Epoch 46/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3754 Epoch 47/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3751 Epoch 48/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3749 Epoch 49/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3746 Epoch 50/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3744 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3741 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3742 Epoch 3/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3741 Epoch 4/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3740 Epoch 5/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3740 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3740 Epoch 7/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3739 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3741 Epoch 9/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 10/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3739 Epoch 11/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3739 Epoch 12/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 13/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3737 Epoch 14/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3738 Epoch 15/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3738 Epoch 16/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3738 Epoch 17/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3737 Epoch 18/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3737 Epoch 19/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 20/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 21/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 22/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 23/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 24/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3735 Epoch 25/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3736 Epoch 26/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3735 Epoch 27/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3735 Epoch 28/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3735 Epoch 29/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3733 Epoch 30/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3734 Epoch 31/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3734 Epoch 32/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3734 Epoch 33/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3732 Epoch 34/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3733 Epoch 35/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3733 Epoch 36/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3733 Epoch 37/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3732 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3733 Epoch 39/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3732 Epoch 40/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 41/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 42/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 43/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 44/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3731 Epoch 45/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 46/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 47/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 48/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 49/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3729 Epoch 50/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 1s 7ms/step - loss: 0.3730 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 4/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 8/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3731 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 11/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3730 Epoch 12/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 13/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3728 Epoch 14/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 15/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 16/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 17/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3729 Epoch 00017: early stopping The 1th layer has been pretrained. Pretraining the 2th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 1ms/step - loss: 0.3967 Epoch 2/50 45/45 [==============================] - 0s 900us/step - loss: 0.2189 Epoch 3/50 45/45 [==============================] - 0s 895us/step - loss: 0.1801 Epoch 4/50 45/45 [==============================] - 0s 878us/step - loss: 0.1613 Epoch 5/50 45/45 [==============================] - 0s 896us/step - loss: 0.1512 Epoch 6/50 45/45 [==============================] - 0s 955us/step - loss: 0.1448 Epoch 7/50 45/45 [==============================] - 0s 931us/step - loss: 0.1399 Epoch 8/50 45/45 [==============================] - 0s 911us/step - loss: 0.1374 Epoch 9/50 45/45 [==============================] - 0s 882us/step - loss: 0.1342 Epoch 10/50 45/45 [==============================] - 0s 889us/step - loss: 0.1318 Epoch 11/50 45/45 [==============================] - 0s 874us/step - loss: 0.1307 Epoch 12/50 45/45 [==============================] - 0s 888us/step - loss: 0.1071 Epoch 13/50 45/45 [==============================] - 0s 911us/step - loss: 0.0879 Epoch 14/50 45/45 [==============================] - 0s 943us/step - loss: 0.0861 Epoch 15/50 45/45 [==============================] - 0s 942us/step - loss: 0.0849 Epoch 16/50 45/45 [==============================] - 0s 919us/step - loss: 0.0844 Epoch 17/50 45/45 [==============================] - 0s 884us/step - loss: 0.0836 Epoch 18/50 45/45 [==============================] - 0s 895us/step - loss: 0.0824 Epoch 19/50 45/45 [==============================] - 0s 884us/step - loss: 0.0809 Epoch 20/50 45/45 [==============================] - 0s 884us/step - loss: 0.0818 Epoch 21/50 45/45 [==============================] - 0s 905us/step - loss: 0.0807 Epoch 22/50 45/45 [==============================] - 0s 910us/step - loss: 0.0799 Epoch 23/50 45/45 [==============================] - 0s 873us/step - loss: 0.0798 Epoch 24/50 45/45 [==============================] - 0s 900us/step - loss: 0.0788 Epoch 25/50 45/45 [==============================] - 0s 871us/step - loss: 0.0782 Epoch 26/50 45/45 [==============================] - 0s 895us/step - loss: 0.0772 Epoch 27/50 45/45 [==============================] - 0s 898us/step - loss: 0.0771 Epoch 28/50 45/45 [==============================] - 0s 891us/step - loss: 0.0769 Epoch 29/50 45/45 [==============================] - 0s 894us/step - loss: 0.0762 Epoch 30/50 45/45 [==============================] - 0s 901us/step - loss: 0.0753 Epoch 31/50 45/45 [==============================] - 0s 961us/step - loss: 0.0759 Epoch 32/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0751 Epoch 33/50 45/45 [==============================] - 0s 999us/step - loss: 0.0752 Epoch 34/50 45/45 [==============================] - 0s 941us/step - loss: 0.0753 Epoch 35/50 45/45 [==============================] - 0s 964us/step - loss: 0.0745 Epoch 36/50 45/45 [==============================] - 0s 939us/step - loss: 0.0739 Epoch 37/50 45/45 [==============================] - 0s 930us/step - loss: 0.0739 Epoch 38/50 45/45 [==============================] - 0s 936us/step - loss: 0.0738 Epoch 39/50 45/45 [==============================] - 0s 940us/step - loss: 0.0732 Epoch 40/50 45/45 [==============================] - 0s 935us/step - loss: 0.0726 Epoch 41/50 45/45 [==============================] - 0s 944us/step - loss: 0.0730 Epoch 42/50 45/45 [==============================] - 0s 936us/step - loss: 0.0732 Epoch 43/50 45/45 [==============================] - 0s 952us/step - loss: 0.0727 Epoch 44/50 45/45 [==============================] - 0s 938us/step - loss: 0.0719 Epoch 45/50 45/45 [==============================] - 0s 926us/step - loss: 0.0723 Epoch 46/50 45/45 [==============================] - 0s 952us/step - loss: 0.0713 Epoch 47/50 45/45 [==============================] - 0s 931us/step - loss: 0.0712 Epoch 48/50 45/45 [==============================] - 0s 934us/step - loss: 0.0707 Epoch 49/50 45/45 [==============================] - 0s 928us/step - loss: 0.0715 Epoch 50/50 45/45 [==============================] - 0s 905us/step - loss: 0.0715 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 968us/step - loss: 0.0711 Epoch 2/50 45/45 [==============================] - 0s 941us/step - loss: 0.0706 Epoch 3/50 45/45 [==============================] - 0s 918us/step - loss: 0.0707 Epoch 4/50 45/45 [==============================] - 0s 904us/step - loss: 0.0711 Epoch 5/50 45/45 [==============================] - 0s 908us/step - loss: 0.0710 Epoch 6/50 45/45 [==============================] - 0s 871us/step - loss: 0.0710 Epoch 7/50 45/45 [==============================] - 0s 914us/step - loss: 0.0709 Epoch 8/50 45/45 [==============================] - 0s 878us/step - loss: 0.0709 Epoch 9/50 45/45 [==============================] - 0s 939us/step - loss: 0.0705 Epoch 10/50 45/45 [==============================] - 0s 875us/step - loss: 0.0699 Epoch 11/50 45/45 [==============================] - 0s 926us/step - loss: 0.0709 Epoch 12/50 45/45 [==============================] - 0s 933us/step - loss: 0.0697 Epoch 13/50 45/45 [==============================] - 0s 912us/step - loss: 0.0699 Epoch 14/50 45/45 [==============================] - 0s 920us/step - loss: 0.0701 Epoch 15/50 45/45 [==============================] - 0s 900us/step - loss: 0.0700 Epoch 16/50 45/45 [==============================] - 0s 932us/step - loss: 0.0705 Epoch 17/50 45/45 [==============================] - 0s 886us/step - loss: 0.0704 Epoch 18/50 45/45 [==============================] - 0s 917us/step - loss: 0.0703 Epoch 19/50 45/45 [==============================] - 0s 890us/step - loss: 0.0695 Epoch 20/50 45/45 [==============================] - 0s 958us/step - loss: 0.0706 Epoch 21/50 45/45 [==============================] - 0s 930us/step - loss: 0.0703 Epoch 22/50 45/45 [==============================] - 0s 924us/step - loss: 0.0701 Epoch 23/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0708 Epoch 24/50 45/45 [==============================] - 0s 881us/step - loss: 0.0703 Epoch 25/50 45/45 [==============================] - 0s 876us/step - loss: 0.0704 Epoch 26/50 45/45 [==============================] - 0s 901us/step - loss: 0.0700 Epoch 27/50 45/45 [==============================] - 0s 912us/step - loss: 0.0705 Epoch 28/50 45/45 [==============================] - 0s 903us/step - loss: 0.0705 Epoch 29/50 45/45 [==============================] - 0s 887us/step - loss: 0.0703 Epoch 00029: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 976us/step - loss: 0.0704 Epoch 2/50 45/45 [==============================] - 0s 953us/step - loss: 0.0701 Epoch 3/50 45/45 [==============================] - 0s 947us/step - loss: 0.0702 Epoch 4/50 45/45 [==============================] - 0s 932us/step - loss: 0.0706 Epoch 5/50 45/45 [==============================] - 0s 922us/step - loss: 0.0706 Epoch 6/50 45/45 [==============================] - 0s 911us/step - loss: 0.0705 Epoch 7/50 45/45 [==============================] - 0s 906us/step - loss: 0.0706 Epoch 8/50 45/45 [==============================] - 0s 911us/step - loss: 0.0706 Epoch 9/50 45/45 [==============================] - 0s 904us/step - loss: 0.0701 Epoch 10/50 45/45 [==============================] - 0s 889us/step - loss: 0.0696 Epoch 11/50 45/45 [==============================] - 0s 940us/step - loss: 0.0706 Epoch 12/50 45/45 [==============================] - 0s 929us/step - loss: 0.0693 Epoch 13/50 45/45 [==============================] - 0s 875us/step - loss: 0.0697 Epoch 14/50 45/45 [==============================] - 0s 889us/step - loss: 0.0698 Epoch 15/50 45/45 [==============================] - 0s 905us/step - loss: 0.0697 Epoch 16/50 45/45 [==============================] - 0s 902us/step - loss: 0.0703 Epoch 17/50 45/45 [==============================] - 0s 910us/step - loss: 0.0701 Epoch 18/50 45/45 [==============================] - 0s 890us/step - loss: 0.0701 Epoch 19/50 45/45 [==============================] - 0s 917us/step - loss: 0.0693 Epoch 20/50 45/45 [==============================] - 0s 899us/step - loss: 0.0704 Epoch 21/50 45/45 [==============================] - 0s 911us/step - loss: 0.0701 Epoch 22/50 45/45 [==============================] - 0s 909us/step - loss: 0.0700 Epoch 00022: early stopping The 2th layer has been pretrained. Copying layer-wise pretrained weights to deep autoencoders Fine-tuning autoencoder end-to-end learning rate = 1 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3707 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3694 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3686 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3680 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3674 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3669 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3664 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3660 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3656 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3652 Epoch 11/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3648 Epoch 12/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3644 Epoch 13/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3640 Epoch 14/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3637 Epoch 15/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3634 Epoch 16/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3630 Epoch 17/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3627 Epoch 18/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3624 Epoch 19/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3621 Epoch 20/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3619 Epoch 21/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3616 Epoch 22/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3613 Epoch 23/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3611 Epoch 24/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3608 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3606 Epoch 26/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3603 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3601 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3599 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3596 Epoch 30/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3594 Epoch 31/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3592 Epoch 32/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3590 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3588 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3586 Epoch 35/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3584 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3582 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3580 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3577 Epoch 40/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3575 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3573 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3572 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3570 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3568 Epoch 45/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3567 Epoch 46/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3565 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3564 Epoch 48/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3562 Epoch 49/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3561 Epoch 50/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3559 learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3555 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3554 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3554 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3554 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3553 Epoch 12/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3552 Epoch 13/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3552 Epoch 14/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3552 Epoch 15/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3552 Epoch 16/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3552 Epoch 17/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3552 Epoch 18/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3552 Epoch 19/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3551 Epoch 20/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3551 Epoch 21/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3551 Epoch 22/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3551 Epoch 23/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3551 Epoch 24/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3551 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3551 Epoch 26/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3550 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 30/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 31/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3550 Epoch 32/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3550 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 35/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 38/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3549 Epoch 40/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3548 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 45/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 46/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3548 Epoch 48/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 49/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3547 Epoch 50/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3547 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 1s 6ms/step - loss: 0.3547 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3547 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3547 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3547 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3547 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 00011: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 00011: early stopping learning rate = 0.0001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 00011: early stopping learning rate = 1e-05 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 8/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3546 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3546 Epoch 00011: early stopping Pretraining time is 77.77368402481079 Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 11 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.052159380772275485 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0894 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0730 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0641 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0568 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0507 The value of delta_label of current 2 th iteration is 0.021110036062978274 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1482 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1251 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1071 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0931 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0821 The value of delta_label of current 3 th iteration is 0.010906851965872108 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1813 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1565 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1367 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1210 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1086 The value of delta_label of current 4 th iteration is 0.011082768933063593 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2061 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1810 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1621 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1479 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1368 The value of delta_label of current 5 th iteration is 0.008883806843170024 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2221 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2034 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1891 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1779 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1687 The value of delta_label of current 6 th iteration is 0.008531972908787053 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2239 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2119 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2020 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1936 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1864 The value of delta_label of current 7 th iteration is 0.0063330108188934826 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2186 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2101 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2027 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1961 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1902 The value of delta_label of current 8 th iteration is 0.005189550532148826 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2114 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2048 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1990 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1937 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1889 The value of delta_label of current 9 th iteration is 0.0031665054094467413 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2041 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1988 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1940 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1897 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1857 The value of delta_label of current 10 th iteration is 0.0024628375406807986 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1972 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1928 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1888 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1852 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1818 The value of delta_label of current 11 th iteration is 0.0015832527047233706 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1907 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1871 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1837 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1807 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1778 The value of delta_label of current 12 th iteration is 0.0013193772539361421 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1848 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1817 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1790 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1764 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1739 The value of delta_label of current 13 th iteration is 0.0010555018031489136 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1794 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1768 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1745 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1723 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1702 delta_label 0.0006157093851701996 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is: 0 2487 1 2235 2 2137 3 1576 4 1252 5 446 6 393 7 331 8 318 9 138 10 56 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_12" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 11) 352 ================================================================= Total params: 277,504 Trainable params: 277,504 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.8)is: 91.67204809188843
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne0.8 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8 into the umap coordinates (adata.obsm)
The run time for all resolution is: 123.88686084747314
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
obsp: 'distances', 'connectivities'
adata
AnnData object with n_obs × n_vars = 11369 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
obsp: 'distances', 'connectivities'
prob_1=adata.uns["prob_matrix0.8"]
adata.obs["max.prob0.8"]=np.max(prob_1,axis=1)
#tSNE plot
sc.pl.scatter(adata,basis="tsne0.8",color=['desc_0.8'])
sc.pl.scatter(adata,basis="tsne0.8",color=["max.prob0.8"], legend_fontoutline=5)
from matplotlib.pyplot import rc_context
with rc_context({'figure.figsize': (5, 5)}):
sc.pl.tsne(adata,color=['desc_0.8',"max.prob0.8"], legend_loc='on data',
legend_fontsize=10, legend_fontoutline=2,frameon=False, title='10x-V3',
add_outline=True, outline_width=(0.5, 0.05), vmin=0.1,vmax=0.8, ncols=1,
save='DESC_Control_Res0.8_TSNE_Prrobabilities.png')
WARNING: The title list is shorter than the number of panels. Using 'color' value instead for some plots. WARNING: saving figure to file figures/tsneDESC_Control_Res0.8_TSNE_Prrobabilities.png
Repeat the exact same framework except switching out the input file from Control to scCLEAN
#input the cellranger output h5ad file from alignment to the full transcriptome
data = desc.read_h5ad('raw_files/FUll_transcriptome/Dep_rep3_not_masked_filtered_feature_bc_matrix.h5ad')
data.var_names_make_unique()
data
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
AnnData object with n_obs × n_vars = 11786 × 36601
var: 'gene_ids', 'feature_types', 'genome'
sc.pp.filter_cells(data, min_counts=500)
sc.pp.filter_cells(data, min_genes=200)
sc.pp.filter_genes(data, min_cells=3)
filtered out 248 cells that have less than 200 genes expressed filtered out 15160 genes that are detected in less than 3 cells
mito_genes = data.var_names.str.startswith('MT-')
# for each cell compute fraction of counts in mito genes vs. all genes
# the `.A1` is only necessary as X is sparse (to transform to a dense array after summing)
data.obs['percent_mito'] = np.sum(
data[:, mito_genes].X, axis=1).A1 / np.sum(data.X, axis=1).A1
# add the total counts per cell as observations-annotation to adata
data.obs['n_counts'] = data.X.sum(axis=1).A1
#determine the proper thresholds according to the 99% of the data
per_cell_metrics = data.obs
dquantile = pd.DataFrame()
dquantile = per_cell_metrics.quantile(0.99, numeric_only=True)
dquantile
n_counts 13217.910000 n_genes 4809.150000 percent_mito 0.001973 Name: 0.99, dtype: float64
Remember the overall counts are lower in the scCLEAN condition because 250 protein coding genes were targeted for removal, and reads were re-distributed to lower expressed transcripts. Consequently, the UMIs associated with housekeeping genes were removed.
sc.pl.violin(data, ['n_genes', 'n_counts', 'percent_mito'],jitter=0.4, multi_panel=True)
#filter thresholds from 99%
data = data[data.obs['n_counts'] < 13217.910000, :]
data
View of AnnData object with n_obs × n_vars = 11422 × 21441
obs: 'n_counts', 'n_genes', 'percent_mito'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells'
desc.normalize_per_cell(data, counts_per_cell_after=1e4)
normalizing by total count per cell
Trying to set attribute `.obs` of view, copying.
finished (0:00:00): normalized adata.X and added 'n_counts', counts per cell before normalization (adata.obs)
desc.log1p(data)
data.raw=data
sc.pp.highly_variable_genes(data, min_mean=0.0125, max_mean=3, min_disp=0.5, subset=True)
extracting highly variable genes
finished (0:00:00)
--> added
'highly_variable', boolean vector (adata.var)
'means', float vector (adata.var)
'dispersions', float vector (adata.var)
'dispersions_norm', float vector (adata.var)
data = data[:, data.var['highly_variable']]
data
View of AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
uns: 'log1p', 'hvg'
desc.scale(data, zero_center=True, max_value=3)
/Users/jbezney/opt/anaconda3/envs/DESC/lib/python3.6/site-packages/scanpy/preprocessing/_simple.py:845: UserWarning: Revieved a view of an AnnData. Making a copy. view_to_actual(adata) ... as `zero_center=True`, sparse input is densified and may lead to large memory consumption
#loop through the deep learning model and append the total number of clusters identified
#check the total number of clusters according to the resolution with which it was identified
resolution_x = [0.1,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,1.8,2.0]
dep_total_clusters = []
for value in resolution_x:
data = desc.train(data, dims=[data.shape[1], 128, 32], tol=0.001, n_neighbors=10,
batch_size=256, louvain_resolution=[value], do_tsne=True, learning_rate=300,
do_umap=True, num_Cores_tsne=4)
df_cluster = pd.DataFrame(data.obs['desc_'+str(value)])
df_cluster = len(df_cluster.iloc[:,0].unique())
dep_total_clusters.append(df_cluster)
Start to process resolution= 0.1 The number of cpu in your computer is 12 Create the directory:result_tmp to save result Checking whether result_tmp/ae_weights.h5 exists in the directory The file ae_weights.h5 is not exits Pretraining the 1th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 1s 7ms/step - loss: 0.4919 Epoch 2/50 45/45 [==============================] - 0s 8ms/step - loss: 0.4660 Epoch 3/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4452 Epoch 4/50 45/45 [==============================] - 0s 8ms/step - loss: 0.4307 Epoch 5/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4200 Epoch 6/50 45/45 [==============================] - 0s 8ms/step - loss: 0.4102 Epoch 7/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4020 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3955 Epoch 9/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3908 Epoch 10/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3872 Epoch 11/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3844 Epoch 12/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3824 Epoch 13/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3805 Epoch 14/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3791 Epoch 15/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3778 Epoch 16/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3767 Epoch 17/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3757 Epoch 18/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3747 Epoch 19/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3740 Epoch 20/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3731 Epoch 21/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3725 Epoch 22/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3717 Epoch 23/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3710 Epoch 24/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3704 Epoch 25/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3697 Epoch 26/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3689 Epoch 27/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3684 Epoch 28/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3678 Epoch 29/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3673 Epoch 30/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3667 Epoch 31/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3663 Epoch 32/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3656 Epoch 33/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3653 Epoch 34/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3648 Epoch 35/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3643 Epoch 36/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3637 Epoch 37/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3634 Epoch 38/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3629 Epoch 39/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3625 Epoch 40/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3621 Epoch 41/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3618 Epoch 42/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3614 Epoch 43/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3611 Epoch 44/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3608 Epoch 45/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3604 Epoch 46/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3600 Epoch 47/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3598 Epoch 48/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3594 Epoch 49/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3592 Epoch 50/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3589 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 2/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3586 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 4/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3586 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3586 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3585 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3584 Epoch 11/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3584 Epoch 12/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3583 Epoch 13/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3583 Epoch 14/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3583 Epoch 15/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 16/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 17/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 18/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 19/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 20/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3581 Epoch 21/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 22/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 23/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3581 Epoch 24/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3581 Epoch 25/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3581 Epoch 26/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3579 Epoch 27/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3580 Epoch 28/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 29/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 30/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 31/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3579 Epoch 32/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3578 Epoch 33/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 34/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 35/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3578 Epoch 36/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3577 Epoch 37/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3578 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3577 Epoch 39/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 40/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 41/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3577 Epoch 42/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 43/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 44/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3576 Epoch 45/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 46/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3575 Epoch 47/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3575 Epoch 48/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3574 Epoch 49/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 50/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3573 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3573 Epoch 4/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3573 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 6/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3574 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3575 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3574 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 11/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3574 Epoch 00011: early stopping The 1th layer has been pretrained. Pretraining the 2th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 1ms/step - loss: 0.3968 Epoch 2/50 45/45 [==============================] - 0s 932us/step - loss: 0.1693 Epoch 3/50 45/45 [==============================] - 0s 970us/step - loss: 0.1313 Epoch 4/50 45/45 [==============================] - 0s 949us/step - loss: 0.1164 Epoch 5/50 45/45 [==============================] - 0s 937us/step - loss: 0.1076 Epoch 6/50 45/45 [==============================] - 0s 972us/step - loss: 0.1024 Epoch 7/50 45/45 [==============================] - 0s 954us/step - loss: 0.0984 Epoch 8/50 45/45 [==============================] - 0s 929us/step - loss: 0.0955 Epoch 9/50 45/45 [==============================] - 0s 967us/step - loss: 0.0932 Epoch 10/50 45/45 [==============================] - 0s 971us/step - loss: 0.0909 Epoch 11/50 45/45 [==============================] - 0s 933us/step - loss: 0.0885 Epoch 12/50 45/45 [==============================] - 0s 944us/step - loss: 0.0866 Epoch 13/50 45/45 [==============================] - 0s 927us/step - loss: 0.0851 Epoch 14/50 45/45 [==============================] - 0s 981us/step - loss: 0.0841 Epoch 15/50 45/45 [==============================] - 0s 955us/step - loss: 0.0831 Epoch 16/50 45/45 [==============================] - 0s 928us/step - loss: 0.0820 Epoch 17/50 45/45 [==============================] - 0s 959us/step - loss: 0.0814 Epoch 18/50 45/45 [==============================] - 0s 989us/step - loss: 0.0799 Epoch 19/50 45/45 [==============================] - 0s 953us/step - loss: 0.0800 Epoch 20/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0787 Epoch 21/50 45/45 [==============================] - 0s 975us/step - loss: 0.0781 Epoch 22/50 45/45 [==============================] - 0s 950us/step - loss: 0.0775 Epoch 23/50 45/45 [==============================] - 0s 991us/step - loss: 0.0772 Epoch 24/50 45/45 [==============================] - 0s 967us/step - loss: 0.0766 Epoch 25/50 45/45 [==============================] - 0s 957us/step - loss: 0.0757 Epoch 26/50 45/45 [==============================] - 0s 924us/step - loss: 0.0759 Epoch 27/50 45/45 [==============================] - 0s 986us/step - loss: 0.0750 Epoch 28/50 45/45 [==============================] - 0s 932us/step - loss: 0.0744 Epoch 29/50 45/45 [==============================] - 0s 958us/step - loss: 0.0746 Epoch 30/50 45/45 [==============================] - 0s 948us/step - loss: 0.0733 Epoch 31/50 45/45 [==============================] - 0s 965us/step - loss: 0.0729 Epoch 32/50 45/45 [==============================] - 0s 967us/step - loss: 0.0730 Epoch 33/50 45/45 [==============================] - 0s 966us/step - loss: 0.0727 Epoch 34/50 45/45 [==============================] - 0s 935us/step - loss: 0.0726 Epoch 35/50 45/45 [==============================] - 0s 969us/step - loss: 0.0716 Epoch 36/50 45/45 [==============================] - 0s 957us/step - loss: 0.0716 Epoch 37/50 45/45 [==============================] - 0s 936us/step - loss: 0.0721 Epoch 38/50 45/45 [==============================] - 0s 978us/step - loss: 0.0709 Epoch 39/50 45/45 [==============================] - 0s 991us/step - loss: 0.0715 Epoch 40/50 45/45 [==============================] - 0s 943us/step - loss: 0.0706 Epoch 41/50 45/45 [==============================] - 0s 982us/step - loss: 0.0707 Epoch 42/50 45/45 [==============================] - 0s 952us/step - loss: 0.0705 Epoch 43/50 45/45 [==============================] - 0s 945us/step - loss: 0.0704 Epoch 44/50 45/45 [==============================] - 0s 984us/step - loss: 0.0696 Epoch 45/50 45/45 [==============================] - 0s 958us/step - loss: 0.0701 Epoch 46/50 45/45 [==============================] - 0s 941us/step - loss: 0.0697 Epoch 47/50 45/45 [==============================] - 0s 992us/step - loss: 0.0695 Epoch 48/50 45/45 [==============================] - 0s 957us/step - loss: 0.0697 Epoch 49/50 45/45 [==============================] - 0s 949us/step - loss: 0.0699 Epoch 50/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0691 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 962us/step - loss: 0.0691 Epoch 2/50 45/45 [==============================] - 0s 920us/step - loss: 0.0689 Epoch 3/50 45/45 [==============================] - 0s 922us/step - loss: 0.0694 Epoch 4/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0690 Epoch 5/50 45/45 [==============================] - 0s 942us/step - loss: 0.0691 Epoch 6/50 45/45 [==============================] - 0s 913us/step - loss: 0.0689 Epoch 7/50 45/45 [==============================] - 0s 921us/step - loss: 0.0689 Epoch 8/50 45/45 [==============================] - 0s 932us/step - loss: 0.0688 Epoch 9/50 45/45 [==============================] - 0s 908us/step - loss: 0.0688 Epoch 10/50 45/45 [==============================] - 0s 923us/step - loss: 0.0692 Epoch 11/50 45/45 [==============================] - 0s 936us/step - loss: 0.0691 Epoch 12/50 45/45 [==============================] - 0s 934us/step - loss: 0.0688 Epoch 13/50 45/45 [==============================] - 0s 917us/step - loss: 0.0684 Epoch 14/50 45/45 [==============================] - 0s 923us/step - loss: 0.0689 Epoch 15/50 45/45 [==============================] - 0s 938us/step - loss: 0.0690 Epoch 16/50 45/45 [==============================] - 0s 917us/step - loss: 0.0689 Epoch 17/50 45/45 [==============================] - 0s 937us/step - loss: 0.0690 Epoch 18/50 45/45 [==============================] - 0s 903us/step - loss: 0.0687 Epoch 19/50 45/45 [==============================] - 0s 933us/step - loss: 0.0693 Epoch 20/50 45/45 [==============================] - 0s 894us/step - loss: 0.0687 Epoch 21/50 45/45 [==============================] - 0s 941us/step - loss: 0.0688 Epoch 22/50 45/45 [==============================] - 0s 925us/step - loss: 0.0688 Epoch 23/50 45/45 [==============================] - 0s 926us/step - loss: 0.0690 Epoch 00023: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0687 Epoch 2/50 45/45 [==============================] - 0s 943us/step - loss: 0.0686 Epoch 3/50 45/45 [==============================] - 0s 950us/step - loss: 0.0691 Epoch 4/50 45/45 [==============================] - 0s 944us/step - loss: 0.0687 Epoch 5/50 45/45 [==============================] - 0s 980us/step - loss: 0.0688 Epoch 6/50 45/45 [==============================] - 0s 971us/step - loss: 0.0686 Epoch 7/50 45/45 [==============================] - 0s 911us/step - loss: 0.0687 Epoch 8/50 45/45 [==============================] - 0s 927us/step - loss: 0.0686 Epoch 9/50 45/45 [==============================] - 0s 926us/step - loss: 0.0685 Epoch 10/50 45/45 [==============================] - 0s 964us/step - loss: 0.0690 Epoch 11/50 45/45 [==============================] - 0s 944us/step - loss: 0.0688 Epoch 12/50 45/45 [==============================] - 0s 954us/step - loss: 0.0686 Epoch 00012: early stopping The 2th layer has been pretrained. Copying layer-wise pretrained weights to deep autoencoders Fine-tuning autoencoder end-to-end learning rate = 1 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3541 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3525 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3515 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3508 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3503 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3497 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3492 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3488 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3483 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3479 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3475 Epoch 12/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3471 Epoch 13/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3466 Epoch 14/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3462 Epoch 15/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3459 Epoch 16/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3455 Epoch 17/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3451 Epoch 18/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3448 Epoch 19/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3445 Epoch 20/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3441 Epoch 21/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3438 Epoch 22/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3435 Epoch 23/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3432 Epoch 24/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3430 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3427 Epoch 26/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3425 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3422 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3420 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3417 Epoch 30/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3415 Epoch 31/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3413 Epoch 32/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3411 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3408 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3406 Epoch 35/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3404 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3402 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3400 Epoch 38/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3398 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3396 Epoch 40/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3395 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3393 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3391 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3389 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3388 Epoch 45/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3386 Epoch 46/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3384 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3383 Epoch 48/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3381 Epoch 49/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3380 Epoch 50/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3378 learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3374 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3373 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3373 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 8/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3372 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 12/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 13/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 14/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 15/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 16/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 17/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 18/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 19/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 20/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 21/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 22/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 23/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 24/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 26/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 30/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 31/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 32/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 35/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 38/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 40/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 45/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3367 Epoch 46/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 48/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 49/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 50/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping learning rate = 0.0001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping learning rate = 1e-05 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping Pretraining time is 75.50488686561584 Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 8 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.03449483452985467 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0931 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0702 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0575 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0487 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0420 The value of delta_label of current 2 th iteration is 0.016897215899142008 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1406 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1140 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0950 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0807 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0698 The value of delta_label of current 3 th iteration is 0.010506040973559796 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1567 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1315 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1131 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0998 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0902 The value of delta_label of current 4 th iteration is 0.009805638241989144 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1629 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1414 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1267 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1163 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1086 The value of delta_label of current 5 th iteration is 0.010506040973559796 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1622 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1489 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1392 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1317 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1257 The value of delta_label of current 6 th iteration is 0.007529329364384521 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1561 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1486 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1425 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1373 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1328 The value of delta_label of current 7 th iteration is 0.003939765365084924 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1488 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1438 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1395 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1356 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1321 The value of delta_label of current 8 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1422 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1384 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1351 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1320 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1292 The value of delta_label of current 9 th iteration is 0.0019261075118192962 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1362 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1332 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1306 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1281 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1257 The value of delta_label of current 10 th iteration is 0.001751006828926633 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1309 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1285 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1263 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1242 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1223 The value of delta_label of current 11 th iteration is 0.0016634564874803011 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1264 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1244 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1226 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1208 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1192 delta_label 0.0009630537559096481 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 4260 1 2062 2 1632 3 1789 4 790 5 388 6 318 7 183 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_15" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 8) 256 ================================================================= Total params: 277,408 Trainable params: 277,408 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.1)is: 87.4849910736084
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:32)
computing neighbors
tsne finished and added X_tsne0.1 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.1 into the umap coordinates (adata.obsm)
The run time for all resolution is: 121.3835871219635
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.016829729080200195
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 9 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.038171948870600596 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0946 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0730 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0605 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0516 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0448 The value of delta_label of current 2 th iteration is 0.01645946419191035 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1416 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1159 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0971 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0830 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0722 The value of delta_label of current 3 th iteration is 0.009017685168972158 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1588 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1340 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1160 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1031 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0937 The value of delta_label of current 4 th iteration is 0.009980738924881808 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1668 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1454 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1308 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1204 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1128 The value of delta_label of current 5 th iteration is 0.009280336193311154 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1683 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1545 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1446 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1369 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1307 The value of delta_label of current 6 th iteration is 0.007879530730169847 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1635 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1555 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1491 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1437 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1391 The value of delta_label of current 7 th iteration is 0.005690772194011557 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1565 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1513 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1469 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1429 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1393 The value of delta_label of current 8 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1500 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1462 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1427 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1396 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1366 The value of delta_label of current 9 th iteration is 0.0025389599019436174 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1442 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1411 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1384 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1358 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1333 The value of delta_label of current 10 th iteration is 0.0014008054631413063 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1390 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1365 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1342 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1321 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1300 The value of delta_label of current 11 th iteration is 0.001225704780248643 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1345 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1325 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1306 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1288 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1271 The value of delta_label of current 12 th iteration is 0.0011381544388023113 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1306 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1289 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1273 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1258 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1243 delta_label 0.0007004027315706532 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
The final prediction cluster is: 0 4271 1 2020 2 1639 3 1785 4 787 5 378 6 300 7 161 8 81 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_16" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 9) 288 ================================================================= Total params: 277,440 Trainable params: 277,440 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.2)is: 13.29884123802185
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne0.2 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.2 into the umap coordinates (adata.obsm)
The run time for all resolution is: 44.709169149398804
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.01116180419921875
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 11 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.04377517072316582 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1021 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0802 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0675 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0585 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.0515 The value of delta_label of current 2 th iteration is 0.031343022237786726 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1564 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1300 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1111 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0967 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0855 The value of delta_label of current 3 th iteration is 0.02775345823848713 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1806 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1561 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1382 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1249 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1149 The value of delta_label of current 4 th iteration is 0.023813692873402206 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1964 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1757 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1610 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1501 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1417 The value of delta_label of current 5 th iteration is 0.019523726142531957 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2069 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1921 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1811 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1726 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1655 The value of delta_label of current 6 th iteration is 0.014620907021537384 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2085 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1983 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1899 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1830 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1770 The value of delta_label of current 7 th iteration is 0.010768691997898792 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.2047 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1970 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1904 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1847 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1796 The value of delta_label of current 8 th iteration is 0.0074417790229381895 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1986 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1927 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1873 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1826 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1784 The value of delta_label of current 9 th iteration is 0.005077919803887235 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1920 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1873 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1831 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1793 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1757 The value of delta_label of current 10 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1857 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1820 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1786 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1756 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1727 The value of delta_label of current 11 th iteration is 0.002451409560497286 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1800 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1771 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1744 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1720 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1696 The value of delta_label of current 12 th iteration is 0.001225704780248643 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1751 Epoch 2/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1727 Epoch 3/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1705 Epoch 4/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1685 Epoch 5/5 45/45 [==============================] - 0s 2ms/step - loss: 0.1665 delta_label 0.0006128523901243215 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 3134 1 2018 2 1628 3 1437 4 782 5 331 6 1488 7 310 8 77 9 145 10 72 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_17" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 11) 352 ================================================================= Total params: 277,504 Trainable params: 277,504 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.4)is: 12.697240114212036
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.4 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.4 into the umap coordinates (adata.obsm)
The run time for all resolution is: 42.61803412437439
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.011688947677612305
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 15 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.06478725267028541 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1202 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0987 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0859 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0766 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0692 The value of delta_label of current 2 th iteration is 0.03633339170022763 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1806 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1562 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1380 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1236 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1121 The value of delta_label of current 3 th iteration is 0.031868324286464716 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2137 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1904 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1726 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1587 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1479 The value of delta_label of current 4 th iteration is 0.02827876028716512 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2366 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2174 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2029 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1915 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1824 The value of delta_label of current 5 th iteration is 0.02889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2552 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2406 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2292 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2200 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2122 The value of delta_label of current 6 th iteration is 0.022587988093153565 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2670 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2559 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2386 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2317 The value of delta_label of current 7 th iteration is 0.018035370337944317 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2723 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2632 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2481 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2418 The value of delta_label of current 8 th iteration is 0.01540886009455437 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2730 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2652 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2520 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2464 The value of delta_label of current 9 th iteration is 0.007704430047277185 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2710 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2643 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2583 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2530 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2480 The value of delta_label of current 10 th iteration is 0.00586587287690422 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2674 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2617 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2566 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2520 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 The value of delta_label of current 11 th iteration is 0.003502013657853266 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2630 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2581 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2538 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2497 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2459 The value of delta_label of current 12 th iteration is 0.003502013657853266 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2539 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2501 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2465 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2430 The value of delta_label of current 13 th iteration is 0.0023638592190509543 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2531 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2493 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2460 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2426 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2395 The value of delta_label of current 14 th iteration is 0.0014008054631413063 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2479 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2445 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2415 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2385 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2356 The value of delta_label of current 15 th iteration is 0.0011381544388023113 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2427 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2397 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2371 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2344 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2319 delta_label 0.0004377517072316582 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 2018 1 1599 2 1794 3 1622 4 615 5 451 6 850 7 334 8 282 9 314 10 1009 11 277 12 65 13 120 14 72 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_18" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 15) 480 ================================================================= Total params: 277,632 Trainable params: 277,632 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.6)is: 15.530126810073853
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.6 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.6 into the umap coordinates (adata.obsm)
The run time for all resolution is: 46.4466278553009
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6'
obsp: 'distances', 'connectivities'
Start to process resolution= 0.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.010951042175292969
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 17 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06907721940115566 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1239 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1028 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0902 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0810 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0738 The value of delta_label of current 2 th iteration is 0.03834704955349326 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1844 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1612 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1450 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1320 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1214 The value of delta_label of current 3 th iteration is 0.03256872701803537 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2178 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1970 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1806 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1675 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1570 The value of delta_label of current 4 th iteration is 0.032481176676589035 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2447 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2256 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2110 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1995 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1903 The value of delta_label of current 5 th iteration is 0.030642619506216075 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2673 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2524 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2408 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2314 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2234 The value of delta_label of current 6 th iteration is 0.0276659078970408 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2821 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2706 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2611 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2530 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2459 The value of delta_label of current 7 th iteration is 0.0224128874102609 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2899 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2804 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2721 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2649 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 The value of delta_label of current 8 th iteration is 0.015759061460339695 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2929 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2848 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2775 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2710 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2651 The value of delta_label of current 9 th iteration is 0.011469094729469446 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2927 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2857 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2793 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2737 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2685 The value of delta_label of current 10 th iteration is 0.007091577657152863 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2904 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2845 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2790 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2742 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2696 The value of delta_label of current 11 th iteration is 0.005253020486779898 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2870 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2820 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2772 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2729 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2689 The value of delta_label of current 12 th iteration is 0.0038522150236385924 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2830 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2786 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2744 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2707 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2672 The value of delta_label of current 13 th iteration is 0.0021887585361582912 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2786 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2748 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2711 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2678 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2647 The value of delta_label of current 14 th iteration is 0.0030642619506216075 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2741 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2707 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2675 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2646 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2617 The value of delta_label of current 15 th iteration is 0.0010506040973559797 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2695 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2665 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2637 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2611 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 The value of delta_label of current 16 th iteration is 0.0011381544388023113 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2651 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2624 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2599 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2575 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 delta_label 0.0004377517072316582 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is:
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
0 1545 1 2014 2 1799 3 1387 4 537 5 452 6 951 7 332 8 280 9 310 10 1037 11 278 12 116 13 147 14 57 15 72 16 108 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_19" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 17) 544 ================================================================= Total params: 277,696 Trainable params: 277,696 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.8)is: 16.651501178741455
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:28)
computing neighbors
tsne finished and added X_tsne0.8 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8 into the umap coordinates (adata.obsm)
The run time for all resolution is: 46.80148506164551
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.0109710693359375
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 20 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.08220977061810542 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1322 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1118 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0996 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0904 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0829 The value of delta_label of current 2 th iteration is 0.04351251969882682 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1987 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1775 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1613 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1480 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1370 The value of delta_label of current 3 th iteration is 0.031605673262125725 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2377 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2170 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2005 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1873 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1765 The value of delta_label of current 4 th iteration is 0.024251444580633864 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2692 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2503 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2357 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2241 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2146 The value of delta_label of current 5 th iteration is 0.02547714936088251 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2933 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2789 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2674 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2579 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2497 The value of delta_label of current 6 th iteration is 0.022675538434599896 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3086 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2976 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2881 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2801 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2729 The value of delta_label of current 7 th iteration is 0.017334967606373666 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3183 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3090 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3007 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2936 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2870 The value of delta_label of current 8 th iteration is 0.013745403607074068 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3242 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3161 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3086 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3020 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2960 The value of delta_label of current 9 th iteration is 0.01006828926632814 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3271 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3199 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3130 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3070 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3015 The value of delta_label of current 10 th iteration is 0.008930134827525827 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3271 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3208 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3148 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3095 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3045 The value of delta_label of current 11 th iteration is 0.005428121169672562 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3251 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3197 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3144 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3098 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3053 The value of delta_label of current 12 th iteration is 0.004114866047977587 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3220 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3172 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3126 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3084 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3044 The value of delta_label of current 13 th iteration is 0.0037646646821922606 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3182 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3140 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3098 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3060 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3024 The value of delta_label of current 14 th iteration is 0.0021887585361582912 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3140 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3102 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3065 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3030 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2997 The value of delta_label of current 15 th iteration is 0.0014008054631413063 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3095 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3061 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3027 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2996 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2966 delta_label 0.0008755034144633164 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is: 0 1464 1 2037 2 1306 3 1385 4 786 5 451 6 326 7 350 8 332 9 164 10 311 11 664 12 1122 13 245 14 101 15 45 16 72 17 221 18 25 19 15 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_20" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 20) 640 ================================================================= Total params: 277,792 Trainable params: 277,792 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.0)is: 16.31411623954773
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:28)
computing neighbors
tsne finished and added X_tsne1.0 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.0 into the umap coordinates (adata.obsm)
The run time for all resolution is: 45.77424669265747
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.012108087539672852
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 20 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06811416564524601 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1361 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1145 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1021 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0928 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0852 The value of delta_label of current 2 th iteration is 0.044212922430397476 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2037 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1831 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1666 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1532 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1423 The value of delta_label of current 3 th iteration is 0.03537033794431798 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2417 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2211 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2045 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1914 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1808 The value of delta_label of current 4 th iteration is 0.028016109262826126 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2734 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2542 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2395 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2279 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2186 The value of delta_label of current 5 th iteration is 0.023200840483277883 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2976 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2829 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2714 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2619 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2539 The value of delta_label of current 6 th iteration is 0.021975135703029242 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3125 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3013 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2919 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2838 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2769 The value of delta_label of current 7 th iteration is 0.016809665557695676 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3215 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3123 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3040 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2968 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2905 The value of delta_label of current 8 th iteration is 0.011994396778147435 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3266 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3186 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3111 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3046 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2989 The value of delta_label of current 9 th iteration is 0.009542987217650149 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3285 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3215 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3147 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3089 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3037 The value of delta_label of current 10 th iteration is 0.007616879705830853 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3277 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3217 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3157 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3107 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3060 The value of delta_label of current 11 th iteration is 0.00534057082822623 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3252 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3199 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3148 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3104 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3063 The value of delta_label of current 12 th iteration is 0.0033269129749606023 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3217 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3171 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3126 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3087 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3050 The value of delta_label of current 13 th iteration is 0.003589563999299597 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3178 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3137 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3097 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3061 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3028 The value of delta_label of current 14 th iteration is 0.0015759061460339696 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3135 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3098 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3063 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3030 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3000 The value of delta_label of current 15 th iteration is 0.0011381544388023113 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3090 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3057 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3026 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2995 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2969 The value of delta_label of current 16 th iteration is 0.0010506040973559797 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3044 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3015 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2986 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2958 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2935 delta_label 0.0008755034144633164 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 1452 1 2039 2 1384 3 1089 4 942 5 782 6 448 7 328 8 353 9 332 10 103 11 314 12 1129 13 242 14 106 15 46 16 72 17 222 18 24 19 15 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_21" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 20) 640 ================================================================= Total params: 277,792 Trainable params: 277,792 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.2)is: 17.398098945617676
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:28)
computing neighbors
tsne finished and added X_tsne1.2 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.2 into the umap coordinates (adata.obsm)
The run time for all resolution is: 46.68986392021179
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.011324882507324219
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 22 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.09954473822447908 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1402 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1199 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1083 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0993 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0919 The value of delta_label of current 2 th iteration is 0.04797758711258974 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2085 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1892 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1735 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1603 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1493 The value of delta_label of current 3 th iteration is 0.03510768691997899 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2479 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2275 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2113 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1981 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1874 The value of delta_label of current 4 th iteration is 0.0293293643845211 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2813 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2629 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2485 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2372 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2278 The value of delta_label of current 5 th iteration is 0.02556469970232884 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3055 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2918 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2807 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2717 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2637 The value of delta_label of current 6 th iteration is 0.02311329014183155 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3201 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3096 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3005 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2929 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2858 The value of delta_label of current 7 th iteration is 0.02031167921554894 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3291 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3201 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3119 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3050 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2984 The value of delta_label of current 8 th iteration is 0.01961127648397829 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3345 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3263 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3188 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3123 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3063 The value of delta_label of current 9 th iteration is 0.018823323410961303 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3367 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3294 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3226 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3166 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3111 The value of delta_label of current 10 th iteration is 0.01540886009455437 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3364 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3300 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3239 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3185 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3135 The value of delta_label of current 11 th iteration is 0.017247417264927335 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3342 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3287 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3232 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3183 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3138 The value of delta_label of current 12 th iteration is 0.01444580633864472 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3309 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3260 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3212 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3168 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3127 The value of delta_label of current 13 th iteration is 0.017247417264927335 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3270 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3226 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3183 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3144 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3106 The value of delta_label of current 14 th iteration is 0.018298021362283312 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3226 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3187 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3149 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3113 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3080 The value of delta_label of current 15 th iteration is 0.01286990019261075 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3178 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3144 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3110 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3078 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3047 The value of delta_label of current 16 th iteration is 0.009455436876203817 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3130 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3098 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3068 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3039 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3011 The value of delta_label of current 17 th iteration is 0.006566275608474873 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3082 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3053 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3025 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2998 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2972 The value of delta_label of current 18 th iteration is 0.006040973559796883 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3034 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3008 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2983 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2958 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2935 The value of delta_label of current 19 th iteration is 0.006828926632813868 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2988 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2965 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2943 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2920 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2899 The value of delta_label of current 20 th iteration is 0.005603221852565225 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2945 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2923 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2903 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2883 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2864 The value of delta_label of current 21 th iteration is 0.003677114340745929 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2902 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2883 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2865 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2847 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2829 The value of delta_label of current 22 th iteration is 0.0033269129749606023 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2863 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2845 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2828 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2812 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2796 The value of delta_label of current 23 th iteration is 0.0021887585361582912 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2825 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2809 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2794 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2779 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2765 The value of delta_label of current 24 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2790 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2775 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2762 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2748 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2735 The value of delta_label of current 25 th iteration is 0.003589563999299597 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2757 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2744 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2732 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2719 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2707 The value of delta_label of current 26 th iteration is 0.0038522150236385924 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2727 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2715 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2704 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2692 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2681 The value of delta_label of current 27 th iteration is 0.0023638592190509543 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2699 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2688 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2677 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2667 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2657 The value of delta_label of current 28 th iteration is 0.002714060584836281 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2672 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2662 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2652 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2643 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2633 The value of delta_label of current 29 th iteration is 0.002714060584836281 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2646 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2637 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2628 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2619 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2611 The value of delta_label of current 30 th iteration is 0.002714060584836281 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2622 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2613 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2605 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2597 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2589 The value of delta_label of current 31 th iteration is 0.0019261075118192962 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2599 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2591 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2576 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2569 The value of delta_label of current 32 th iteration is 0.0018385571703729644 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2578 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2571 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2564 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2557 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2550 The value of delta_label of current 33 th iteration is 0.0014883558045876379 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2558 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2545 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2538 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 The value of delta_label of current 34 th iteration is 0.0033269129749606023 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2534 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2528 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2522 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2516 The value of delta_label of current 35 th iteration is 0.003151812292067939 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2523 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2517 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2512 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2506 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2500 The value of delta_label of current 36 th iteration is 0.0019261075118192962 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2507 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2502 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2497 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2491 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2486 The value of delta_label of current 37 th iteration is 0.003151812292067939 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2492 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2487 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2478 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2473 The value of delta_label of current 38 th iteration is 0.003151812292067939 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2478 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2474 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2469 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2465 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2460 The value of delta_label of current 39 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2465 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2461 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2457 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2453 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2449 The value of delta_label of current 40 th iteration is 0.0033269129749606023 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2453 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2449 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2445 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2441 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2437 The value of delta_label of current 41 th iteration is 0.005690772194011557 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2442 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2438 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2434 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2430 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2427 The value of delta_label of current 42 th iteration is 0.006828926632813868 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2431 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2427 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2423 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2420 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2416 The value of delta_label of current 43 th iteration is 0.014008054631413063 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2420 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2417 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2413 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2410 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2407 The value of delta_label of current 44 th iteration is 0.01278234985116442 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2410 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2407 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2404 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2400 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2397 The value of delta_label of current 45 th iteration is 0.02031167921554894 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2400 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2397 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2394 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2391 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2388 The value of delta_label of current 46 th iteration is 0.013220101558396077 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2391 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2388 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2386 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2383 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2380 The value of delta_label of current 47 th iteration is 0.010593591315006128 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2382 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2380 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2377 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2374 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2372 The value of delta_label of current 48 th iteration is 0.010768691997898792 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2374 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2371 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2369 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2366 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2364 The value of delta_label of current 49 th iteration is 0.008404832778847838 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2366 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2364 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2361 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2359 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2356 The value of delta_label of current 50 th iteration is 0.005778322535457888 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2358 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2356 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2353 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2351 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2349 The value of delta_label of current 51 th iteration is 0.0040273157065312554 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2351 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2348 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2346 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2344 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2342 The value of delta_label of current 52 th iteration is 0.0038522150236385924 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2343 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2341 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2339 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2337 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2335 The value of delta_label of current 53 th iteration is 0.001751006828926633 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2336 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2334 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2332 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2330 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2328 delta_label 0.0007879530730169848 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is: 0 1941 1 1381 2 2048 3 980 4 5 5 887 6 763 7 449 8 335 9 355 10 329 11 312 12 2 13 635 14 251 15 109 16 46 17 72 18 221 19 256 20 30 21 15 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_22" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 22) 704 ================================================================= Total params: 277,856 Trainable params: 277,856 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.4)is: 50.433396100997925
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne1.4 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.4 into the umap coordinates (adata.obsm)
The run time for all resolution is: 80.59438610076904
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.01788020133972168
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 23 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.1012957450534057 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1405 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1203 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1087 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0999 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0926 The value of delta_label of current 2 th iteration is 0.04403782174750481 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2089 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1900 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1747 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1618 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1511 The value of delta_label of current 3 th iteration is 0.03361933111539135 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2475 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2280 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2123 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1995 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1891 The value of delta_label of current 4 th iteration is 0.029241814043074767 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2807 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2629 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2490 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2379 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2287 The value of delta_label of current 5 th iteration is 0.026352652775345823 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3055 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2921 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2811 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2722 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2644 The value of delta_label of current 6 th iteration is 0.02285063911749256 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3213 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3109 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3020 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2944 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2875 The value of delta_label of current 7 th iteration is 0.019786377166870952 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3315 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3225 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3145 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3076 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3012 The value of delta_label of current 8 th iteration is 0.021012081947119593 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3383 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3303 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3229 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3164 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3103 The value of delta_label of current 9 th iteration is 0.01768516897215899 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3422 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3349 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3281 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3221 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3166 The value of delta_label of current 10 th iteration is 0.019786377166870952 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3433 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3369 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3308 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3254 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3203 The value of delta_label of current 11 th iteration is 0.021274732971458588 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3424 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3367 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3312 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3262 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3216 The value of delta_label of current 12 th iteration is 0.019961477849763615 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3403 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3352 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3303 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3257 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3215 The value of delta_label of current 13 th iteration is 0.0138329539485204 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3373 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3327 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3283 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3241 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3203 The value of delta_label of current 14 th iteration is 0.010243389949220801 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3337 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3296 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3256 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3217 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3182 The value of delta_label of current 15 th iteration is 0.009805638241989144 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3296 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3258 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3222 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3187 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3154 The value of delta_label of current 16 th iteration is 0.00639117492558221 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3252 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3217 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3185 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3153 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3122 The value of delta_label of current 17 th iteration is 0.005953423218350551 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3206 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3174 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3145 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3116 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3088 The value of delta_label of current 18 th iteration is 0.006040973559796883 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3159 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3131 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3104 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3079 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3054 The value of delta_label of current 19 th iteration is 0.0051654701453335665 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3113 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3088 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3065 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3042 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3020 The value of delta_label of current 20 th iteration is 0.004727718438101909 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3069 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3047 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3026 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3005 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2985 The value of delta_label of current 21 th iteration is 0.003151812292067939 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3028 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3007 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2988 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2969 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2951 The value of delta_label of current 22 th iteration is 0.0032393626335142705 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2988 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2969 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2951 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2934 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2918 The value of delta_label of current 23 th iteration is 0.0023638592190509543 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2950 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2933 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2917 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2901 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2886 The value of delta_label of current 24 th iteration is 0.0032393626335142705 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2915 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2899 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2884 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2870 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2856 The value of delta_label of current 25 th iteration is 0.0023638592190509543 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2881 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2867 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2853 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2840 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2827 The value of delta_label of current 26 th iteration is 0.0015759061460339696 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2849 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2836 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2823 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2811 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2800 The value of delta_label of current 27 th iteration is 0.002714060584836281 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2819 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2807 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2795 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2784 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2774 The value of delta_label of current 28 th iteration is 0.002451409560497286 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2790 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2779 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2769 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2758 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2749 The value of delta_label of current 29 th iteration is 0.0022763088776046225 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2763 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2753 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2743 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2734 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2725 The value of delta_label of current 30 th iteration is 0.003677114340745929 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2738 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2729 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2719 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2710 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2702 The value of delta_label of current 31 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2714 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2705 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2697 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2688 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2681 The value of delta_label of current 32 th iteration is 0.003151812292067939 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2691 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2683 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2675 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2668 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2660 The value of delta_label of current 33 th iteration is 0.004289966730870251 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2670 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2663 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2656 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2648 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2642 The value of delta_label of current 34 th iteration is 0.0032393626335142705 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2650 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2643 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2637 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2630 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2624 The value of delta_label of current 35 th iteration is 0.004202416389423919 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2632 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2625 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2619 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2613 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2607 The value of delta_label of current 36 th iteration is 0.0021887585361582912 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2614 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2609 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2603 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2597 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2591 The value of delta_label of current 37 th iteration is 0.0030642619506216075 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2598 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2592 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2587 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2576 The value of delta_label of current 38 th iteration is 0.002626510243389949 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2577 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2572 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2567 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2562 The value of delta_label of current 39 th iteration is 0.004289966730870251 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2567 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2563 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2558 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2553 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2548 The value of delta_label of current 40 th iteration is 0.0032393626335142705 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2554 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2549 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2544 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2536 The value of delta_label of current 41 th iteration is 0.003151812292067939 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2536 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2527 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2523 The value of delta_label of current 42 th iteration is 0.002451409560497286 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2528 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2523 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2519 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2515 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2511 The value of delta_label of current 43 th iteration is 0.003414463316406934 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2515 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2511 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2507 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2504 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2500 The value of delta_label of current 44 th iteration is 0.005603221852565225 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2504 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2500 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2496 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2493 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 The value of delta_label of current 45 th iteration is 0.005953423218350551 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2492 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2486 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2479 The value of delta_label of current 46 th iteration is 0.008667483803186833 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2479 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2476 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2472 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2469 The value of delta_label of current 47 th iteration is 0.013132551216949746 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2472 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2469 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2463 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2461 The value of delta_label of current 48 th iteration is 0.016371913850464017 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2463 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2460 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2458 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2455 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2452 The value of delta_label of current 49 th iteration is 0.021274732971458588 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2455 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2452 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2450 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2447 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2444 The value of delta_label of current 50 th iteration is 0.025389599019436177 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2447 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2444 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2442 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2439 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2437 The value of delta_label of current 51 th iteration is 0.01602171248467869 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2439 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2437 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2435 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2432 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2430 The value of delta_label of current 52 th iteration is 0.007004027315706532 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2432 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2430 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2428 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2425 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2423 The value of delta_label of current 53 th iteration is 0.005253020486779898 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2425 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2423 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2421 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2419 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2417 The value of delta_label of current 54 th iteration is 0.003151812292067939 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2419 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2417 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2415 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2413 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2411 The value of delta_label of current 55 th iteration is 0.0014008054631413063 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2413 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2411 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2409 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2407 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2405 delta_label 0.0 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 1942 1 1381 2 1984 3 938 4 898 5 769 6 449 7 332 8 654 9 351 10 329 11 1 12 297 13 247 14 109 15 44 16 292 17 72 18 220 19 67 20 31 21 15 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_23" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 23) 736 ================================================================= Total params: 277,888 Trainable params: 277,888 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.6)is: 53.03005409240723
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.6 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.6 into the umap coordinates (adata.obsm)
The run time for all resolution is: 83.80500197410583
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6'
obsp: 'distances', 'connectivities'
Start to process resolution= 1.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.012325048446655273
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 23 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.10488530905270531 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1404 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1198 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1080 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0992 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0919 The value of delta_label of current 2 th iteration is 0.04745228506391175 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2081 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1888 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1734 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1607 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1501 The value of delta_label of current 3 th iteration is 0.035983190334442305 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2468 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2273 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2116 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1988 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1883 The value of delta_label of current 4 th iteration is 0.032481176676589035 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2799 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2619 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2479 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2368 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2276 The value of delta_label of current 5 th iteration is 0.02827876028716512 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3045 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2908 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2800 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2710 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2631 The value of delta_label of current 6 th iteration is 0.026615303799684818 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3197 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3093 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3004 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2928 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2858 The value of delta_label of current 7 th iteration is 0.022062686044475574 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3292 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3203 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3124 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3055 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2991 The value of delta_label of current 8 th iteration is 0.02031167921554894 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3351 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3271 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3198 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3134 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3074 The value of delta_label of current 9 th iteration is 0.021099632288565925 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3381 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3309 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3242 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3182 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3127 The value of delta_label of current 10 th iteration is 0.020749430922780598 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3384 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3320 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3260 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3206 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3156 The value of delta_label of current 11 th iteration is 0.023288390824724215 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3370 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3313 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3259 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3211 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3165 The value of delta_label of current 12 th iteration is 0.022675538434599896 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3345 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3294 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3246 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3203 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3160 The value of delta_label of current 13 th iteration is 0.01768516897215899 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3315 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3270 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3226 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3187 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3149 The value of delta_label of current 14 th iteration is 0.013920504289966731 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3281 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3241 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3202 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3167 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3131 The value of delta_label of current 15 th iteration is 0.009980738924881808 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3247 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3210 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3175 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3143 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3110 The value of delta_label of current 16 th iteration is 0.007791980388723516 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3212 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3178 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3146 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3116 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3087 The value of delta_label of current 17 th iteration is 0.007354228681491858 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3176 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3146 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3115 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3088 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3061 The value of delta_label of current 18 th iteration is 0.004552617755209245 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3140 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3112 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3084 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3059 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3033 The value of delta_label of current 19 th iteration is 0.007004027315706532 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3103 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3078 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3053 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3030 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3007 The value of delta_label of current 20 th iteration is 0.004289966730870251 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3066 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3044 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3021 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3000 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2979 The value of delta_label of current 21 th iteration is 0.003414463316406934 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3029 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3009 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2989 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2970 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2951 The value of delta_label of current 22 th iteration is 0.0033269129749606023 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2993 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2975 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2957 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2940 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2922 The value of delta_label of current 23 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2958 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2941 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2925 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2909 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2894 The value of delta_label of current 24 th iteration is 0.0028016109262826126 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2924 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2909 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2894 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2880 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2866 The value of delta_label of current 25 th iteration is 0.0032393626335142705 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2892 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2878 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2864 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2851 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2838 The value of delta_label of current 26 th iteration is 0.0029767116091752757 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2862 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2849 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2836 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2824 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2812 The value of delta_label of current 27 th iteration is 0.002889161267728944 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2832 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2821 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2809 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2798 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2787 The value of delta_label of current 28 th iteration is 0.004114866047977587 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2805 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2794 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2783 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2773 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2763 The value of delta_label of current 29 th iteration is 0.003502013657853266 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2779 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2769 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2759 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2749 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2739 The value of delta_label of current 30 th iteration is 0.002451409560497286 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2754 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2745 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2735 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2726 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2717 The value of delta_label of current 31 th iteration is 0.0032393626335142705 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2730 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2722 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2713 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2705 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2697 The value of delta_label of current 32 th iteration is 0.003414463316406934 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2708 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2700 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2692 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2685 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2677 The value of delta_label of current 33 th iteration is 0.0033269129749606023 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2688 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2680 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2673 Epoch 4/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2666 Epoch 5/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2659 The value of delta_label of current 34 th iteration is 0.00481526877954824 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2668 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2661 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2655 Epoch 4/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2648 Epoch 5/5 45/45 [==============================] - 0s 4ms/step - loss: 0.2641 The value of delta_label of current 35 th iteration is 0.0021887585361582912 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2650 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2644 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2637 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2631 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2625 The value of delta_label of current 36 th iteration is 0.002451409560497286 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2633 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2627 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2621 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2615 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2609 The value of delta_label of current 37 th iteration is 0.0032393626335142705 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2616 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2611 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2605 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2600 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2594 The value of delta_label of current 38 th iteration is 0.0029767116091752757 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2600 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2595 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2590 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2585 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2579 The value of delta_label of current 39 th iteration is 0.0018385571703729644 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2585 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2580 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2575 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2571 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2565 The value of delta_label of current 40 th iteration is 0.0028016109262826126 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2571 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2566 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2561 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2557 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2552 The value of delta_label of current 41 th iteration is 0.00481526877954824 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2557 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2553 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2548 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2544 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 The value of delta_label of current 42 th iteration is 0.011031343022237787 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2544 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2536 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2528 The value of delta_label of current 43 th iteration is 0.009893188583435476 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2528 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2524 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2520 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2516 The value of delta_label of current 44 th iteration is 0.015583960777447031 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2520 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2517 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2513 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2509 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2506 The value of delta_label of current 45 th iteration is 0.016722115216249344 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2509 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2506 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2502 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2499 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2495 The value of delta_label of current 46 th iteration is 0.016722115216249344 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2499 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2496 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2492 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2486 The value of delta_label of current 47 th iteration is 0.014095604972859395 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2489 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2486 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2483 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2480 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 The value of delta_label of current 48 th iteration is 0.008930134827525827 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2480 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2474 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2471 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2468 The value of delta_label of current 49 th iteration is 0.0019261075118192962 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2471 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2468 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2465 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2462 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2459 delta_label 0.0009630537559096481 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 1947 1 1382 2 2017 3 5 4 976 5 473 6 766 7 448 8 330 9 354 10 331 11 615 12 11 13 295 14 681 15 242 16 101 17 43 18 72 19 220 20 68 21 30 22 15 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_24" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 23) 736 ================================================================= Total params: 277,888 Trainable params: 277,888 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=1.8)is: 49.09917163848877
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.8 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.8 into the umap coordinates (adata.obsm)
The run time for all resolution is: 80.43619990348816
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8'
obsp: 'distances', 'connectivities'
Start to process resolution= 2.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5 exists in the directory
Pretraining time is 0.01738119125366211
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 27 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.13920504289966731 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 1s 3ms/step - loss: 0.1458 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1258 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1147 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1062 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0991 The value of delta_label of current 2 th iteration is 0.06741376291367536 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2176 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1994 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1847 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1725 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1621 The value of delta_label of current 3 th iteration is 0.04964104360007004 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2579 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2399 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2251 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2129 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2027 The value of delta_label of current 4 th iteration is 0.04079845911399054 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2941 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2773 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2640 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2533 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2442 The value of delta_label of current 5 th iteration is 0.0445631237961828 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3222 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3088 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2979 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2889 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2809 The value of delta_label of current 6 th iteration is 0.04920329189283838 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3402 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3295 Epoch 3/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3203 Epoch 4/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3125 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3053 The value of delta_label of current 7 th iteration is 0.04736473472246542 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3512 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3421 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3340 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3269 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3202 The value of delta_label of current 8 th iteration is 0.03256872701803537 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3569 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3489 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3415 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3349 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3287 The value of delta_label of current 9 th iteration is 0.029767116091752758 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3591 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3518 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3451 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3390 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3333 The value of delta_label of current 10 th iteration is 0.02941691472596743 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3587 Epoch 2/5 45/45 [==============================] - 0s 5ms/step - loss: 0.3524 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3465 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3410 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3358 The value of delta_label of current 11 th iteration is 0.031868324286464716 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3570 Epoch 2/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3516 Epoch 3/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3463 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3414 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3368 The value of delta_label of current 12 th iteration is 0.024776746629311855 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3545 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3497 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3450 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3406 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3365 The value of delta_label of current 13 th iteration is 0.021537383995797584 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3515 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3473 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3430 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3390 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3352 The value of delta_label of current 14 th iteration is 0.015671511118893363 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3480 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3443 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3404 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3368 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3334 The value of delta_label of current 15 th iteration is 0.014270705655752057 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3443 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3409 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3374 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3341 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3310 The value of delta_label of current 16 th iteration is 0.0138329539485204 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3403 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3373 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3340 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3310 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3282 The value of delta_label of current 17 th iteration is 0.013570302924181404 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3362 Epoch 2/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3335 Epoch 3/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3305 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3278 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3252 The value of delta_label of current 18 th iteration is 0.009192785851864822 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3320 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3296 Epoch 3/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3269 Epoch 4/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3244 Epoch 5/5 45/45 [==============================] - 0s 4ms/step - loss: 0.3220 The value of delta_label of current 19 th iteration is 0.010768691997898792 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3280 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3257 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3232 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3210 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3188 The value of delta_label of current 20 th iteration is 0.01006828926632814 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3240 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3219 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3196 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3176 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3155 The value of delta_label of current 21 th iteration is 0.010418490632113465 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3201 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3182 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3161 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3142 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3123 The value of delta_label of current 22 th iteration is 0.008317282437401506 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3164 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3146 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3127 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3109 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3092 The value of delta_label of current 23 th iteration is 0.0074417790229381895 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3128 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3111 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3094 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3077 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3060 The value of delta_label of current 24 th iteration is 0.008667483803186833 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3094 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3078 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3061 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3045 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3030 The value of delta_label of current 25 th iteration is 0.008579933461740501 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3059 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3045 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3029 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3015 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3000 The value of delta_label of current 26 th iteration is 0.006216074242689547 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3026 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.3012 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2998 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2984 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2971 The value of delta_label of current 27 th iteration is 0.005778322535457888 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2994 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2981 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2967 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2955 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2943 The value of delta_label of current 28 th iteration is 0.005953423218350551 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2963 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2951 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2939 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2927 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2916 The value of delta_label of current 29 th iteration is 0.006040973559796883 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2934 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2924 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2912 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2902 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2891 The value of delta_label of current 30 th iteration is 0.006216074242689547 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2908 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2898 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2887 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2877 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2867 The value of delta_label of current 31 th iteration is 0.005778322535457888 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2883 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2873 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2864 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2854 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2845 The value of delta_label of current 32 th iteration is 0.005253020486779898 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2859 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2850 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2841 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2833 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2825 The value of delta_label of current 33 th iteration is 0.004289966730870251 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2837 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2829 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2821 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2813 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2805 The value of delta_label of current 34 th iteration is 0.006040973559796883 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2816 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2808 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2801 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2793 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2786 The value of delta_label of current 35 th iteration is 0.0051654701453335665 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2796 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2789 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2782 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2775 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2769 The value of delta_label of current 36 th iteration is 0.004289966730870251 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2777 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2770 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2764 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2758 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2751 The value of delta_label of current 37 th iteration is 0.004902819120994572 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2759 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2753 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2747 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2741 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2735 The value of delta_label of current 38 th iteration is 0.005077919803887235 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2742 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2736 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2730 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2725 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2719 The value of delta_label of current 39 th iteration is 0.003939765365084924 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2726 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2720 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2714 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2709 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2704 The value of delta_label of current 40 th iteration is 0.006303624584135878 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2710 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2704 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2699 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2694 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2689 The value of delta_label of current 41 th iteration is 0.005778322535457888 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2694 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2689 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2684 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2679 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2674 The value of delta_label of current 42 th iteration is 0.008930134827525827 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2679 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2675 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2670 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2665 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2660 The value of delta_label of current 43 th iteration is 0.01444580633864472 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2665 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2660 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2656 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2651 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2647 The value of delta_label of current 44 th iteration is 0.023726142531955874 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2651 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2647 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2642 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2638 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2634 The value of delta_label of current 45 th iteration is 0.03318157940815969 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2638 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2634 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2630 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2626 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2622 The value of delta_label of current 46 th iteration is 0.039835405358080896 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2626 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2622 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2618 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2614 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2610 The value of delta_label of current 47 th iteration is 0.03239362633514271 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2614 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2610 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2607 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2603 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2599 The value of delta_label of current 48 th iteration is 0.023726142531955874 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2603 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2599 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2596 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2592 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2589 The value of delta_label of current 49 th iteration is 0.00963053755909648 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2592 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2589 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2586 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2579 The value of delta_label of current 50 th iteration is 0.007879530730169847 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2582 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2579 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2576 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2573 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2570 The value of delta_label of current 51 th iteration is 0.007179127998599194 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2573 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2570 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2567 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2564 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2561 The value of delta_label of current 52 th iteration is 0.00849238312029417 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2564 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2561 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2558 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2555 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2553 The value of delta_label of current 53 th iteration is 0.008755034144633165 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2555 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2552 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2550 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2547 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2545 The value of delta_label of current 54 th iteration is 0.015146209070215374 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2547 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2544 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2542 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2540 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2537 The value of delta_label of current 55 th iteration is 0.016809665557695676 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2539 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2537 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2535 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2530 The value of delta_label of current 56 th iteration is 0.022500437751707233 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2532 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2530 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2527 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2525 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2523 The value of delta_label of current 57 th iteration is 0.025126947995097182 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2525 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2523 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2520 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2518 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2516 The value of delta_label of current 58 th iteration is 0.02451409560497286 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2518 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2516 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2514 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2512 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2510 The value of delta_label of current 59 th iteration is 0.024776746629311855 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2511 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2509 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2507 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2505 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2503 The value of delta_label of current 60 th iteration is 0.02013657853265628 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2505 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2503 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2501 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2499 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2497 The value of delta_label of current 61 th iteration is 0.019523726142531957 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2499 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2497 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2495 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2493 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2492 The value of delta_label of current 62 th iteration is 0.01812292067939065 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2493 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2491 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2490 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2488 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2486 The value of delta_label of current 63 th iteration is 0.015759061460339695 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2487 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2486 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2484 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2480 The value of delta_label of current 64 th iteration is 0.014270705655752057 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2482 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2480 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2478 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2477 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2475 The value of delta_label of current 65 th iteration is 0.016371913850464017 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2476 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2475 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2473 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2471 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2470 The value of delta_label of current 66 th iteration is 0.014095604972859395 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2471 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2470 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2468 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2465 The value of delta_label of current 67 th iteration is 0.01961127648397829 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2466 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2465 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2463 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2461 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2460 The value of delta_label of current 68 th iteration is 0.019348625459639293 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2461 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2460 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2458 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2456 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2455 The value of delta_label of current 69 th iteration is 0.012432148485379093 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2456 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2455 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2453 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2452 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2450 The value of delta_label of current 70 th iteration is 0.009718087900542812 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2452 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2450 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2449 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2447 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2446 The value of delta_label of current 71 th iteration is 0.006566275608474873 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2447 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2445 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2444 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2443 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2441 The value of delta_label of current 72 th iteration is 0.001751006828926633 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2442 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2441 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2440 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2438 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2437 delta_label 0.0001751006828926633 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model. The final prediction cluster is: 0 2068 1 1336 2 2140 3 914 4 651 5 761 6 448 7 310 8 365 9 405 10 329 11 1 12 294 13 234 14 2 15 254 16 402 17 183 18 48 19 99 20 21 21 72 22 49 23 21 24 15 dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_25" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 27) 864 ================================================================= Total params: 278,016 Trainable params: 278,016 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=2.0)is: 70.00197196006775
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne2.0 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap2.0 into the umap coordinates (adata.obsm)
The run time for all resolution is: 100.4626030921936
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8', 'desc_2.0'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8', 'prob_matrix2.0'
obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8', 'X_Embeded_z2.0', 'X_tsne2.0', 'X_umap2.0'
obsp: 'distances', 'connectivities'
dep_total_clusters
[8, 9, 11, 15, 17, 20, 20, 22, 22, 23, 25]
#go back and pick a resolution in the middle (0.8) to highlight
data = desc.train(data, dims=[data.shape[1], 128, 32], tol=0.001, n_neighbors=10,
batch_size=256, louvain_resolution=0.8, do_tsne=True, learning_rate=300,
do_umap=True, num_Cores_tsne=4)
Start to process resolution= 0.8 The number of cpu in your computer is 12 Create the directory:result_tmp to save result Checking whether result_tmp/ae_weights.h5 exists in the directory The file ae_weights.h5 is not exits Pretraining the 1th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 1s 7ms/step - loss: 0.4919 Epoch 2/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4660 Epoch 3/50 45/45 [==============================] - 0s 8ms/step - loss: 0.4452 Epoch 4/50 45/45 [==============================] - 0s 8ms/step - loss: 0.4307 Epoch 5/50 45/45 [==============================] - 0s 7ms/step - loss: 0.4200 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.4102 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.4020 Epoch 8/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3955 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3908 Epoch 10/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3872 Epoch 11/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3844 Epoch 12/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3824 Epoch 13/50 45/45 [==============================] - 0s 9ms/step - loss: 0.3805 Epoch 14/50 45/45 [==============================] - 0s 10ms/step - loss: 0.3791 Epoch 15/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3778 Epoch 16/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3767 Epoch 17/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3757 Epoch 18/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3747 Epoch 19/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3740 Epoch 20/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3731 Epoch 21/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3725 Epoch 22/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3717 Epoch 23/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3710 Epoch 24/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3704 Epoch 25/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3697 Epoch 26/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3689 Epoch 27/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3684 Epoch 28/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3678 Epoch 29/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3673 Epoch 30/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3667 Epoch 31/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3663 Epoch 32/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3656 Epoch 33/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3653 Epoch 34/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3648 Epoch 35/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3643 Epoch 36/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3637 Epoch 37/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3634 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3629 Epoch 39/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3625 Epoch 40/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3621 Epoch 41/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3618 Epoch 42/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3614 Epoch 43/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3611 Epoch 44/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3608 Epoch 45/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3604 Epoch 46/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3600 Epoch 47/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3598 Epoch 48/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3594 Epoch 49/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3592 Epoch 50/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3589 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3586 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 4/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3586 Epoch 6/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3586 Epoch 8/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3585 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3584 Epoch 11/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3584 Epoch 12/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3583 Epoch 13/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3583 Epoch 14/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3583 Epoch 15/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3582 Epoch 16/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3582 Epoch 17/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3582 Epoch 18/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3582 Epoch 19/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3582 Epoch 20/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3581 Epoch 21/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3582 Epoch 22/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3582 Epoch 23/50 45/45 [==============================] - 0s 7ms/step - loss: 0.3581 Epoch 24/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3581 Epoch 25/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3581 Epoch 26/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 27/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3580 Epoch 28/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 29/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 30/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 31/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 32/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3578 Epoch 33/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 34/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3579 Epoch 35/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3578 Epoch 36/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3577 Epoch 37/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3578 Epoch 38/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3577 Epoch 39/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 40/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 41/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3577 Epoch 42/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 43/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 44/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 45/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3576 Epoch 46/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3575 Epoch 47/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3575 Epoch 48/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 49/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 50/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3573 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 3/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3573 Epoch 4/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3573 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3574 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3575 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3574 Epoch 9/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3574 Epoch 10/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3574 Epoch 11/50 45/45 [==============================] - 0s 8ms/step - loss: 0.3574 Epoch 00011: early stopping The 1th layer has been pretrained. Pretraining the 2th layer... learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 970us/step - loss: 0.3968 Epoch 2/50 45/45 [==============================] - 0s 890us/step - loss: 0.1693 Epoch 3/50 45/45 [==============================] - 0s 887us/step - loss: 0.1313 Epoch 4/50 45/45 [==============================] - 0s 939us/step - loss: 0.1164 Epoch 5/50 45/45 [==============================] - 0s 923us/step - loss: 0.1076 Epoch 6/50 45/45 [==============================] - 0s 971us/step - loss: 0.1024 Epoch 7/50 45/45 [==============================] - 0s 997us/step - loss: 0.0984 Epoch 8/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0955 Epoch 9/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0932 Epoch 10/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0909 Epoch 11/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0885 Epoch 12/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0866 Epoch 13/50 45/45 [==============================] - 0s 989us/step - loss: 0.0851 Epoch 14/50 45/45 [==============================] - 0s 986us/step - loss: 0.0841 Epoch 15/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0831 Epoch 16/50 45/45 [==============================] - 0s 971us/step - loss: 0.0820 Epoch 17/50 45/45 [==============================] - 0s 967us/step - loss: 0.0814 Epoch 18/50 45/45 [==============================] - 0s 964us/step - loss: 0.0799 Epoch 19/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0800 Epoch 20/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0787 Epoch 21/50 45/45 [==============================] - 0s 953us/step - loss: 0.0781 Epoch 22/50 45/45 [==============================] - 0s 953us/step - loss: 0.0775 Epoch 23/50 45/45 [==============================] - 0s 917us/step - loss: 0.0772 Epoch 24/50 45/45 [==============================] - 0s 933us/step - loss: 0.0766 Epoch 25/50 45/45 [==============================] - 0s 923us/step - loss: 0.0757 Epoch 26/50 45/45 [==============================] - 0s 929us/step - loss: 0.0759 Epoch 27/50 45/45 [==============================] - 0s 956us/step - loss: 0.0750 Epoch 28/50 45/45 [==============================] - 0s 934us/step - loss: 0.0744 Epoch 29/50 45/45 [==============================] - 0s 937us/step - loss: 0.0746 Epoch 30/50 45/45 [==============================] - 0s 914us/step - loss: 0.0733 Epoch 31/50 45/45 [==============================] - 0s 899us/step - loss: 0.0729 Epoch 32/50 45/45 [==============================] - 0s 893us/step - loss: 0.0730 Epoch 33/50 45/45 [==============================] - 0s 905us/step - loss: 0.0727 Epoch 34/50 45/45 [==============================] - 0s 893us/step - loss: 0.0726 Epoch 35/50 45/45 [==============================] - 0s 930us/step - loss: 0.0716 Epoch 36/50 45/45 [==============================] - 0s 957us/step - loss: 0.0716 Epoch 37/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0721 Epoch 38/50 45/45 [==============================] - 0s 983us/step - loss: 0.0709 Epoch 39/50 45/45 [==============================] - 0s 985us/step - loss: 0.0715 Epoch 40/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0706 Epoch 41/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0707 Epoch 42/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0705 Epoch 43/50 45/45 [==============================] - 0s 991us/step - loss: 0.0704 Epoch 44/50 45/45 [==============================] - 0s 972us/step - loss: 0.0696 Epoch 45/50 45/45 [==============================] - 0s 993us/step - loss: 0.0701 Epoch 46/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0697 Epoch 47/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0695 Epoch 48/50 45/45 [==============================] - 0s 984us/step - loss: 0.0697 Epoch 49/50 45/45 [==============================] - 0s 985us/step - loss: 0.0699 Epoch 50/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0691 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0691 Epoch 2/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0689 Epoch 3/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0694 Epoch 4/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0690 Epoch 5/50 45/45 [==============================] - 0s 993us/step - loss: 0.0691 Epoch 6/50 45/45 [==============================] - 0s 928us/step - loss: 0.0689 Epoch 7/50 45/45 [==============================] - 0s 928us/step - loss: 0.0689 Epoch 8/50 45/45 [==============================] - 0s 970us/step - loss: 0.0688 Epoch 9/50 45/45 [==============================] - 0s 964us/step - loss: 0.0688 Epoch 10/50 45/45 [==============================] - 0s 943us/step - loss: 0.0692 Epoch 11/50 45/45 [==============================] - 0s 935us/step - loss: 0.0691 Epoch 12/50 45/45 [==============================] - 0s 921us/step - loss: 0.0688 Epoch 13/50 45/45 [==============================] - 0s 915us/step - loss: 0.0684 Epoch 14/50 45/45 [==============================] - 0s 952us/step - loss: 0.0689 Epoch 15/50 45/45 [==============================] - 0s 930us/step - loss: 0.0690 Epoch 16/50 45/45 [==============================] - 0s 922us/step - loss: 0.0689 Epoch 17/50 45/45 [==============================] - 0s 903us/step - loss: 0.0690 Epoch 18/50 45/45 [==============================] - 0s 901us/step - loss: 0.0687 Epoch 19/50 45/45 [==============================] - 0s 907us/step - loss: 0.0693 Epoch 20/50 45/45 [==============================] - 0s 940us/step - loss: 0.0687 Epoch 21/50 45/45 [==============================] - 0s 941us/step - loss: 0.0688 Epoch 22/50 45/45 [==============================] - 0s 939us/step - loss: 0.0688 Epoch 23/50 45/45 [==============================] - 0s 880us/step - loss: 0.0690 Epoch 00023: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0687 Epoch 2/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0686 Epoch 3/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0691 Epoch 4/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0687 Epoch 5/50 45/45 [==============================] - 0s 1ms/step - loss: 0.0688 Epoch 6/50 45/45 [==============================] - 0s 977us/step - loss: 0.0686 Epoch 7/50 45/45 [==============================] - 0s 950us/step - loss: 0.0687 Epoch 8/50 45/45 [==============================] - 0s 933us/step - loss: 0.0686 Epoch 9/50 45/45 [==============================] - 0s 913us/step - loss: 0.0685 Epoch 10/50 45/45 [==============================] - 0s 902us/step - loss: 0.0690 Epoch 11/50 45/45 [==============================] - 0s 916us/step - loss: 0.0688 Epoch 12/50 45/45 [==============================] - 0s 926us/step - loss: 0.0686 Epoch 00012: early stopping The 2th layer has been pretrained. Copying layer-wise pretrained weights to deep autoencoders Fine-tuning autoencoder end-to-end learning rate = 1 Epoch 1/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3541 Epoch 2/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3525 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3515 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3508 Epoch 5/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3503 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3497 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3492 Epoch 8/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3488 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3483 Epoch 10/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3479 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3475 Epoch 12/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3471 Epoch 13/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3466 Epoch 14/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3462 Epoch 15/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3459 Epoch 16/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3455 Epoch 17/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3451 Epoch 18/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3448 Epoch 19/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3445 Epoch 20/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3441 Epoch 21/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3438 Epoch 22/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3435 Epoch 23/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3432 Epoch 24/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3430 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3427 Epoch 26/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3425 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3422 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3420 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3417 Epoch 30/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3415 Epoch 31/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3413 Epoch 32/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3411 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3408 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3406 Epoch 35/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3404 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3402 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3400 Epoch 38/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3398 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3396 Epoch 40/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3395 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3393 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3391 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3389 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3388 Epoch 45/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3386 Epoch 46/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3384 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3383 Epoch 48/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3381 Epoch 49/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3380 Epoch 50/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3378 learning rate = 0.1 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3374 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3373 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3373 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3372 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 12/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 13/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 14/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 15/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 16/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3371 Epoch 17/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 18/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 19/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 20/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 21/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 22/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 23/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 24/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3370 Epoch 25/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 26/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 27/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 28/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 29/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 30/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 31/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3369 Epoch 32/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 33/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 34/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 35/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 36/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 37/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 38/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3368 Epoch 39/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 40/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 41/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 42/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 43/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 44/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 45/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3367 Epoch 46/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 47/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 48/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 49/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 Epoch 50/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3366 learning rate = 0.01 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping learning rate = 0.001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 6ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping learning rate = 0.0001 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping learning rate = 1e-05 Epoch 1/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 2/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 3/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 4/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 5/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 6/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 7/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 8/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 9/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 10/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 11/50 45/45 [==============================] - 0s 5ms/step - loss: 0.3365 Epoch 00011: early stopping Pretraining time is 71.79617214202881 Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
using the "louvain" package of Traag (2017)
finished: found 17 clusters and added
'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06907721940115566 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1239 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1028 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0902 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0810 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.0738 The value of delta_label of current 2 th iteration is 0.03834704955349326 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1844 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1612 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1450 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1320 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1214 The value of delta_label of current 3 th iteration is 0.03256872701803537 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2178 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1970 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1806 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1675 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1570 The value of delta_label of current 4 th iteration is 0.032481176676589035 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2447 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2256 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2110 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1995 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.1903 The value of delta_label of current 5 th iteration is 0.030642619506216075 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2673 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2524 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2408 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2314 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2234 The value of delta_label of current 6 th iteration is 0.0276659078970408 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2821 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2706 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2611 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2530 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2459 The value of delta_label of current 7 th iteration is 0.0224128874102609 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2899 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2804 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2721 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2649 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 The value of delta_label of current 8 th iteration is 0.015759061460339695 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2929 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2848 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2775 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2710 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2651 The value of delta_label of current 9 th iteration is 0.011469094729469446 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2927 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2857 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2793 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2737 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2685 The value of delta_label of current 10 th iteration is 0.007091577657152863 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2904 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2845 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2790 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2742 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2696 The value of delta_label of current 11 th iteration is 0.005253020486779898 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2870 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2820 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2772 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2729 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2689 The value of delta_label of current 12 th iteration is 0.0038522150236385924 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2830 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2786 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2744 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2707 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2672 The value of delta_label of current 13 th iteration is 0.0021887585361582912 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2786 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2748 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2711 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2678 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2647 The value of delta_label of current 14 th iteration is 0.0030642619506216075 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2741 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2707 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2675 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2646 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2617 The value of delta_label of current 15 th iteration is 0.0010506040973559797 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2695 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2665 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2637 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2611 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2584 The value of delta_label of current 16 th iteration is 0.0011381544388023113 >= tol 0.001 Epoch 1/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2651 Epoch 2/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2624 Epoch 3/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2599 Epoch 4/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2575 Epoch 5/5 45/45 [==============================] - 0s 3ms/step - loss: 0.2551 delta_label 0.0004377517072316582 < tol 0.001 Reached tolerance threshold. Stop training. WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is: 0 1545 1 2014 2 1799 3 1387 4 537 5 452 6 951 7 332 8 280 9 310 10 1037 11 278 12 116 13 147 14 57 15 72 16 108 dtype: int64 The desc has been trained successfully!!!!!! The summary of desc model is: Model: "model_15" _________________________________________________________________ Layer (type) Output Shape Param # ================================================================= input (InputLayer) [(None, 2132)] 0 _________________________________________________________________ encoder_0 (Dense) (None, 128) 273024 _________________________________________________________________ encoder_1 (Dense) (None, 32) 4128 _________________________________________________________________ clustering (ClusteringLayer) (None, 17) 544 ================================================================= Total params: 277,696 Trainable params: 277,696 Non-trainable params: 0 _________________________________________________________________ The runtime of (resolution=0.8)is: 88.80368900299072
finished: added
'X_tsne', tSNE coordinates (adata.obsm) (0:00:32)
computing neighbors
tsne finished and added X_tsne0.8 into the umap coordinates (adata.obsm)
finished: added to `.uns['neighbors']`
`.obsp['distances']`, distances for each pair of neighbors
`.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
finished: added
'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8 into the umap coordinates (adata.obsm)
The run time for all resolution is: 122.48604488372803
After training, the information of adata is:
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
obsp: 'distances', 'connectivities'
data
AnnData object with n_obs × n_vars = 11422 × 2132
obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
obsp: 'distances', 'connectivities'
prob_1=data.uns["prob_matrix0.8"]
data.obs["max.prob0.8"]=np.max(prob_1,axis=1)
#tSNE plot
sc.pl.scatter(data,basis="tsne0.8",color=['desc_0.8'])
sc.pl.scatter(data,basis="tsne0.8",color=["max.prob0.8"], legend_fontoutline=5)
from matplotlib.pyplot import rc_context
with rc_context({'figure.figsize': (5, 5)}):
sc.pl.tsne(data,color=['desc_0.8',"max.prob0.8"], legend_loc='on data',
legend_fontsize=10, legend_fontoutline=2,frameon=False, title='scCLEAN',
add_outline=True, outline_width=(0.5, 0.05), vmin=0.1,vmax=0.8, ncols=1,
save='DESC_Depleted_Res0.8_TSNE_Prrobabilities.png')
WARNING: The title list is shorter than the number of panels. Using 'color' value instead for some plots. WARNING: saving figure to file figures/tsneDESC_Depleted_Res0.8_TSNE_Prrobabilities.png
